United States Environmental Protection Agency
                Office of Water
                Office of Environmental Information
                Washington, DC
                EPA No. 841-R-09-004
   National Coastal Condition Assessment
            Quality Assurance
                Project Plan
July 2010

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Quality Assurance Project Plan for                                          July 2010
National Coastal Condition Assessment                                        Page ii
                   QUALITY ASSURANCE PROJECT PLAN


              REVIEW & DISTRIBUTION ACKNOWLEDGMENT AND
                        COMMITMENT TO IMPLEMENT

                                     for

                   National Coastal Condition Assessment
We have read the QAPP and the methods manuals for the National Coastal Condition
Assessment listed below. Our agency/organization agrees to abide by its requirements
for work performed under the National Coastal Condition Assessment

      Quality Assurance Project Plan   n
      Field Operations Manual        n
      Site Evaluation Guidelines       n
      Laboratory Methods Manual     n
Print Name
Title
(Cooperator's Principal Investigator)
Organization
Signature                                                         Date

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National Coastal Condition Assessment                                           Page iii
                                     NOTICES

The National Coastal Condition Assessment (NCCA) monitoring and assessment project and
this Quality Assurance Project Plan (QAPP) are based on the previous Environmental
Monitoring and Assessment Program's (EMAP) National Coastal Assessment (NCA) conducted
in 2001 - 2004. The QAPP has been revised to reflect updated personnel lists, several revised
indicators and protocols, and the transfer of lead responsibility from the Office of Research and
Development (ORD) during the research survey phase to the Office of Water (OW) in the
implementation phase with technical support from ORD. Much of this document was modeled
as originally written for the National Coastal Assessment Quality Assurance Project Plan 2001 -
2004 and other National Surveys (the Wadeable Streams Assessment, the National Lakes
Assessment, and the National Rivers and Streams Assessment), where appropriate.

The complete documentation of overall NCCA project management, design, methods, and
standards is contained in four companion documents, including:

   •  National Coastal Condition Assessment: Quality Assurance Project Plan (EPA 841-R-09-004)
   •  National Coastal Condition Assessment: Field Operations  Manual (EPA 21010A)
   •  National Coastal Condition Assessment: Laboratory Methods Manual (EPA, 201 OB)
   •  National Coastal Condition Assessment: Site Evaluation Guidelines (EPA, 201OC)

This document (QAPP) contains elements of the overall project management, data quality
objectives, measurement and data acquisition, and information management for the NCCA.
Methods described in this document are to be used specifically in work relating to the NCCA.
All Project Cooperators should follow these guidelines. Mention of trade names or commercial
products in this document does not constitute endorsement or recommendation for use. More
details on specific methods for site evaluation, field sampling, and  laboratory processing can be
found in the appropriate companion document(s).

The citation for this document is:

U.S. EPA.  2009. National Coastal Condition Assessment Quality Assurance Project Plan 2008-
2012. United States Environmental Protection Agency, Office of Water, Office of Wetlands,
Oceans  and Watersheds. Washington, D.C. EPA/841-R-09-004.

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                                    ABSTRACT

The National Coastal Condition Assessment is one of a series of water assessments being
conducted by states, tribes, the U.S. Environmental Protection Agency (EPA), and other
partners. In addition to coastal waters, the water assessments will also focus on rivers and
streams, lakes, and wetlands in a revolving  sequence. The purpose of these assessments is to
generate statistically valid reports on the condition of our Nation's water resources and identify
key stressors to these systems.

A first step in the development of this type of program was the initiation of EPA's EMAP. This
program laid the groundwork for the National Coastal Assessment program, a national coastal
monitoring program organized and executed at the state level.  The Great Lakes have been
added to this round of assessments and is included in the final  NCCA report projected to be
released in 2012.

This document is the QAPP for the  National Coastal Condition Assessment program. This
QAPP was prepared and formatted in accordance with the guidelines presented in EPA
Requirements for Quality Assurance Project Plans for Environmental Data Operations (EPA
QA/R-5), U.S. EPA Quality Management Staff (U.S. EPA, 1993). According to the type of work
to be performed and the intended use of the data, four categories have been defined that vary
the level of detail and rigor prescribed for a  particular QAPP. This document was prepared for a
Category II Project: Complementary Support to Rulemaking, Regulation, or Policy Decisions.
Such projects are of sufficient scope and robustness that their results can be combined with
those from other projects of similar scope to provide the necessary information for decisions.

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National Coastal Condition Assessment                                          Page v
                               SIGNATURE PAGE
Gregory Colianni                                                      Date
NCCA Project Manager
Treda Grayson                                                        Date
NCCA Project Co-Manager
Joe Hall                                                             Date
Project Quality Assurance Officer
Charles Spooner                                                      Date
OWOW Quality Assurance Officer
Sarah Lehmann                                                       Date
National Aquatic Resource Surveys (NARS) Team Leader

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National Coastal Condition Assessment                                           Page vi
                                Table of Contents

NOTICES	iii
ABSTRACT	iv
SIGNATURE PAGE	v
ACRONYMS	xiv
DISTRIBUTION LIST	xvi
1.    Project Planning and Management	1
      1.1.    I ntroduction	1
      1.2.    National Coastal Condition Assessment Project Organization	2
      1.3.    Study Design	12
             1.3.1.  Project Schedule	13
      1.4.    Scope of QA Project Plan	14
             1.4.1.  Overview of Field Operations	14
             1.4.2.  Overview of Laboratory Operations	17
             1.4.3.  Data Analysis and Reporting	20
             1.4.4.  Peer Review	20
2.    Data Quality Objectives	21
      2.1.    Data Quality Objectives for the National Coastal Condition Assessment	22
      2.2.    Measurement Quality Objectives	22
             2.2.1.  Method  Detection Limits (Laboratory Reporting Level (Sensitivity))	22
             2.2.2.  Sampling Precision, Bias, and Accuracy	23
             2.2.3.  Taxonomic Precision and Accuracy	25
             2.2.4.  Completeness	26
             2.2.5.  Comparability	26
             2.2.6.  Representativeness	27
3.    Site Selection Design	27
      3.1.    Probability Based Sampling Design and Site Selection	28
             3.1.1.  Survey Design for the Marine Waters	28
             3.1.2.  Survey Design for the Great Lakes	29
             3.1.3.  Revisit Sites	29

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4.     Information Management	29
       4.1.    Roles and Responsibilities	30
             4.1.1.  State-Based Data Management	32
       4.2.    Overview of System Structure	33
             4.2.1.  Data Flow Conceptual Model	33
             4.2.2.  Simplified Data Flow Description	34
       4.3.    Core Information Management Standards	36
             4.3.1.  Data Formats	36
             4.3.2.  Public Accessibility	37
       4.4.    Data Transfer Protocols	38
       4.5.    Data Quality and Results Validation	39
             4.5.1.  Data Entry, Scanned, or Transferred Data	39
             4.5.2.  Analytical Results Validation	40
             4.5.3.  Database Changes	40
       4.6.    Metadata	41
       4.7.    Information Management Operations	41
             4.7.1.  Computing Infrastructure	41
             4.7.2.  Data Security and Accessibility	41
             4.7.3.  Life Cycle	41
             4.7.4.  Data Recovery and Emergency Backup Procedures	42
             4.7.5.  Long-Term Data Accessibility and Archive	42
       4.8.    Records Management	42
5.     Indicators	42
       5.1.    I ndicator Summary	42
             5.1.1.  I ntroduction	42
             5.1.2.  Sampling Design	43
             5.1.3.  Sampling and Analytical Methods	43
             5.1.4.  Quality Assurance Objectives	43
             5.1.5.  Quality Control Procedures:  Field Operations	43
             5.1.6.  Quality Control Procedures:  Laboratory Operations	44
       5.2.    In Situ Measurements	45
             5.2.1.  I ntroduction	45
             5.2.2.  Sampling Design	46
             5.2.3.  Sampling and Analytical Methods	46

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             5.2.4.  Quality Assurance Objectives	47
             5.2.5.  Quality Control  Procedures: Field Operations	48
             5.2.6.  Quality Control  Procedures: Laboratory Operations	54
             5.2.7.  Data Reporting, Review, and Management	54
       5.3.   Water Quality Measurements	55
             5.3.1.  Introduction	55
             5.3.2.  Sampling Design	56
             5.3.3.  Sampling and Analytical Methods	56
             5.3.4.  Quality Assurance Objectives	57
             5.3.5.  Quality Control  Procedures: Field Operations	59
             5.3.6.  Quality Control  Procedures: Laboratory Operations	61
             5.3.7.  Data Reporting, Review, and Management	66
       5.4.   Benthic Macrovinvertebrates	68
             5.4.1.  Introduction	68
             5.4.2.  Sampling Design	68
             5.4.3.  Sampling and Analytical Methods	68
             5.4.4.  Quality Assurance Objectives	69
             5.4.5.  Quality Control  Procedures: Field Operations	70
             5.4.6.  Quality Control  Procedures: Laboratory Operations	70
             5.4.7.  Data Reporting, Review and Management	74
       5.5.   Sediment and Fish Sampling and Chemistry	74
             5.5.1.  Introduction	74
             5.5.2.  Sampling Design	75
             5.5.3.  Sampling and Analytical Methods	80
             5.5.4.  Quality Assurance Objectives	83
             5.5.5.  Quality Control  Procedures: Field Operations	85
             5.5.6.  Quality Control  Procedures: Laboratory Operations	87
             5.5.7.  Data Reporting, Review and Management	89
       5.6.   Sediment Grain Size and TOC	90
             5.6.1.  Introduction	90
             5.6.2.  Sampling Design	90
             5.6.3.  Sampling and Analytical Methods	90
             5.6.4.  Quality Assurance Objectives	91
             5.6.5.  Quality Control  Procedures: Field Operations	91
             5.6.6.  Quality Control  Procedures: Laboratory Operations	92

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             5.6.7.  Data Reporting, Review and Management	94
       5.7.   Sediment Toxicity	95
             5.7.1.  I ntroduction	95
             5.7.2.  Sampling Design	95
             5.7.3.  Sampling and Analytical Methods	95
             5.7.4.  Quality Assurance Objectives	95
             5.7.5.  Quality Control Procedures: Field Operations	96
             5.7.6.  Quality Control Procedures: Laboratory Operations	96
             5.7.7.  Data Reporting, Review and Management	98
       5.8.   Pathogen Indicator	99
             5.8.1.  Introduction	99
             5.8.2.  Sampling Design	100
             5.8.3.  Sampling and Analytical Methods	100
             5.8.4.  Quality Assurance Objectives	101
             5.8.5.  Quality Control Procedures: Field Operations	102
             5.8.6.  Quality Control Procedures: Laboratory Operations	102
             5.8.7.  Data Reporting, Review and Management	104
       5.9.   Site Characteristics	104
6.     Field and Biological Quality Evaluation & Assistance Visits	104
       6.1    Field Quality Evaluation and Assistance Visit Plan for the NCCA	106
       6.2.   Laboratory Quality Evaluation and Assistance Visit Plan for the NCCA	108
7.     Data Analysis Plan	113
       7.1.   Data Interpretation Background	113
             7.1.1.  Scale of Assessment	113
             7.1.2.  Selecting Indicators	113
       7.2.   Datasets to be used for the Report	114
       7.3.   Indicators for the Coastal Assessment	114
             7.3.1.  Water Chemistry and Chlorophyll	114
             7.3.2.  Benthic Macroinvertebrates	114
             7.3.3.  Sediment Chemistry/Characteristics	114
             7.3.4.  Enterococci Data Analysis	114
             7.3.5.  Fish Chemistry	115
       7.4.   NCCR Index Development Approach	115
       7.5.   Calculation of Population Estimates	115

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       7.6.   Relative Extent, Relative Risk and Attributable Risk Analysis	115
       7.7.   Other Change Analyses	115
       7.8.   Index Precision and Interpretation	116
8.     References	117

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Quality Assurance Project Plan for
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July 2010
  Page xi
                                    LIST OF TABLES
Table 1.2-1.   Contact List	7
Table 4.1      Summary of IM Responsibilities	44
Table 5.2-1.   NCCA In situ Indicators	46
Table 5.2-2.   Measurement data quality objectives: water chemistry indicator	48
Table 5.2-3.   Field quality control: CTD indicator	51
Table 5.2-4.   Field quality control: multiparameter meter indicator	53
Table 5.2-5.   Data reporting criteria: field measurements	55
Table 5.3-1.   National Coastal Condition Assessment Indicators	55
Table 5.3-2.   Measurement data quality objectives: water chemistry indicator	58
Table 5.3-3.   Measurement data quality objectives: phytoplankton indicator	59
Table 5.3-4.   Sample processing quality control activities: water chemistry indicator	60
Table 5.3-5.   Sample processing quality control: chlorophyll a indicator	61
Table 5.3-6.   Sample processing quality control: phytoplankton indicator	61
Table 5.3-7.   Sample receipt and processing quality control: water chemistry indicator	62
Table 5.3-8.   Laboratory quality control samples:  water chemistry indicator	64
Table 5.3-9.   Laboratory quality control samples:  chlorophyll a indicator	65
Table 5.3-10.  Laboratory quality control samples:  phytoplankton indicator	66
Table 5.3-11.  Data validation quality control: water chemistry, chlorophyll a and
              phytoplankton indicators	67
Table 5.3-12.  Data reporting criteria: water chemistry indicator	67
Table 5.3-13.  Data reporting criteria: chlorophyll-a indicator	68
Table 5.4-1.   Measurement data quality objectives: benthic indicator	69
Table 5.4-2.   Sample collection and field processing quality control: benthic indicator	70
Table 5.4-3.   Sample receipt and processing quality control: benthic Macroinvertebrate
              indicator	71
Table 5.4-4.   Laboratory Quality Control: benthic  macroinvertebrate sample processing	73
Table 5.4-5.   Laboratory Quality Control: benthic  macroinvertebrate taxonomic identification.73
Table 5.4-6.   Data review, verification, and validation quality control: benthic indicator	74
Table 5.5-1.   Recommended target species for whole body fish tissue collection by specific
              biogeographical region	77
Table 5.5-2.   Target Fish Species for Great Lakes HH fish tissue composites	79
Table 5.5-3.   Indicator List of Metals (sediment and eco-fish tissue)	81
Table 5.5-4.   Indicator List of Organchlorine Pesticides (sediment and eco-fish tussue)	81

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Table 5.5-5.   Indicator List of PCBs (sediment and eco-fish tissue)	82
Table 5.5-6.   Indicator List of PAHs (sediment only) 	82
Table 5.5-7.   Indicator List for Human Health Fish Tissue Only	83
Table 5.5-8.   Field Data Types: Sediment and Fish Tissue Indicators	83
Table 5.5-9.   Measurement quality objectives for fish tissue and sediment indicators	84
Table 5.5-10.  Target Method Detection Limits (MDLs) for laboratory analyses
              NCCA samples	85
Table 5.5-11.  Sample collection and field processing quality control: sediment
              chemistry indicator	86
Table 5.5-12.  Field quality control: fish tissue indicator	86
Table 5.5-13.  Sample receipt and processing quality control: sediment and fish
              tissue chemistry samples	87
Table 5.5-14.  Laboratory QC protocols	88
Table 5.5-15.  Data validation quality control: sediment composite	89
Table 5.5-16.  Data validation quality control: eco-fish tissue indicator	89
Table 5.5-17.  Data Reporting Criteria: Sediment and Eco-Fish Tissue Chemistry	90
Table 5.6-1.   Measurement quality objectives forTOC and grain size indicators	91
Table 5.6-2.   Sample collection and field processing quality control: sediment TOC
              and grain size indicator	92
Table 5.6-3.   Sample receipt and processing quality control: TOC and grain size  indicators...93
Table 5.6-4.   Laboratory QC protocols for sediment TOC  and grain size indicators	94
Table 5.6-5.   Data validation quality control: sediment TOC and grain size	94
Table 5.6-6.   Data Reporting Criteria: Sediment Tests	95
Table 5.7-1.   Measurement quality objectives for sediment toxicity indicator	96
Table 5.7-2.   Sample collection and field processing quality control: sediment
              toxicity indicator	96
Table 5.7-3.   Sample receipt and processing quality control: sediment toxicity indicator	97
Table 5.7-4.   Data validation quality control: sediment toxicity	99
Table 5.7-5.   Data Reporting Criteria: Sediment and Fish  Tissue Chemistry	99
Table 5.8-1.   Field and laboratory methods: pathogen indicator (Enterococci) 	100
Table 5.8-2.   Measurement data quality objectives: Pathogen-Indicator DMA Sequences ....101
Table 5.8-3.   Sample collection and field processing quality control: fecal indicator	102
Table 5.8-4.   Laboratory Quality Control: Pathogen-Indicator DMA Sequences	103
Table 5.8-5.   Data validation quality control: fecal indicator	104
Table 7.1.     Criteria for Assessing Dissolved Inorganic Nitrogen	116

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Quality Assurance Project Plan for
National Coastal Condition Assessment
July 2010
 Page xiii
                                 LIST OF FIGURES
Figure 1.1.    NCCA Project Organization	11
Figure 1.2.    NCCA Marine Base Sites	12
Figure 1.3.    NCCA Great Lakes Coastal Base Sites	13
Figure 1.4.    Site Evaluation Diagram	16
Figure 4.1.    Organization of the National Aquatic Resource Surveys Information
             Management System (NARSIMS) for the NCCA	34
Figure 4.2.    Conceptual model of data flow into and out of the master SQL database
             for the NCCA	35
Figure 5.2-1.  Field Chemistry Measurement Procedures	50
Figure 5.3-1.  Laboratory Sample Processing	63

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                                   ACRONYMS

APHA    American Public Health Association
ASCII    American Standard Code for Information Interchange
CAS     Chemical Abstracts Service
CRM     Certified Reference Material
CSDGM  Content Standards for Digital Geospatial Metadata
CV      Coefficient of Variation
DDT     dichlorodiphenyltrichloroethane
DO      Dissolved Oxygen
DQOs    Data Quality Objectives
EMAP    Environmental Monitoring and Assessment Program
FGDC    Federal Geographic Data Committee
FOIA     Freedom of Information Act
GC      Gas Chromatograph
GED     Gulf Ecology Division
GLEC    Great Lakes Environmental Center, Inc.
GPS     Global Positioning System
GRTS    Generalized Random Tessellation Stratified
ICP      Inductively Coupled Plasma
IDL      Instrument Detection Limit
IM       Information Management
IT IS     Integrated Taxonomic Information System
LDR     Linear Dynamic Range
LRL     Laboratory Reporting Level
LT-MDL  Long-term Method Detection Limit
MDLs    Method Detection Limits
MQOs    Measurement Quality Objectives
NARSIMS National Aquatic Resource Surveys Information Management System
NARS    National Aquatic Resource Surveys
NCA     National Coastal Assessment (past surveys)
NCCA    National Coastal Condition Assessment (current survey)
NCCRs   National Coastal Condition Reports
NELAC   National Environmental Laboratory Accreditation Conference
NEP     National Estuary Programs
NERL    U.S. EPA New England Regional Laboratory
NHD     National Hydrography Dataset
NHEERL National Health and Environmental Effects Research Laboratory
NIST     National Institute of Standards and Technology
NOAA    National Oceanic and Atmospheric Administration
NRCC    National Research Council of Canada

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NWQL    National Water Quality Laboratory
OARM    Office of Administrative Resource Management
ORD      Office of Research and Development
OST      Office of Science and Technology
OW       Off ice of Water
OWOW   Office of Wetlands, Oceans and Watersheds
PAHs     Polycyclic Aromatic Hydrocarbons
PAR      Photosynthetically Active Radiation
PBDE     Polybrominated Diphenyl Ethers
PCBs     Polychlorinated biphenyl
PE        Performance Evaluation
PFC      Perfluorinated compound
PPT      parts per thousand
PSU      Practical Salinity Unit
PTD      Percent Taxonomic Disagreement
QAPP     Quality Assurance Project Plan
QA/QC    Quality Assurance/Quality Control
qPCR     quantitative Polymerase Chain Reaction
R-EMAP   Regional Environmental Monitoring and Assessment Program
RSD      Relative Standard Deviation
SAS      Statistical Analysis System
SDTS     Spatial Data Transfer Standard
SQL      Structure Query Language
SRM      Standard Reference Material
STORET  Storage and Retrieval Data Warehouse
SWIMS   Surface Water Information  Management System
TKN      Total Kjeldahl Nitrogen
TOC      Total Organic Carbon
TSA      Technical Systems Audits
US EPA   United States Environmental Protection Agency
USGS     United Stated Geological Survey
WED      Western Ecology Division
WQX      Water Quality Exchange

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Quality Assurance Project Plan for
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                               Page xvi
                                  DISTRIBUTION LIST

This QAPP and associated manuals or guidelines will be distributed to the following: EPA,
States, Tribes, universities, and contractors participating in the NCCA. EPA Regional NCCA
Coordinators are responsible for distributing the NCCA QAPP to State and Tribal Water Quality
Agency staff or other cooperators who will perform the field sampling and laboratory operations.
Great Lakes Environmental Center (GLEC) and Tetra Tech QA Officers will distribute the QAPP
and associated documents to participating project staff at their respective facilities and to the
project contacts at participating laboratories, as they are determined Copies also will be made
available, upon request, to anyone genuinely interested in the quality program for the NCCA.
The document will also be available on EPA's website.
         Darvene Adams, Region II
         Richard Batuik, CBP
         Paul Bertram, GLNPO
         Greg Colianni, OW
         Philip Crocker, Region VI
         Ed Decker, Region IV
         Lorraine Edmond, Region X
         Terrence Fleming, Region IX
         Treda Grayson, OW
         Janet Hashimoto, Region IX
         Linda Harwell, ORD
         Gretchen Hayslip, Region X
         Laura Hunt, Region VI
         Eric Hyatt, Region VIM
         Jack Kelly, ORD
         Sarah Lehmann, OW
                                       U.S. EPA
Catherine Libertz, Region III
Cindy Lin, Region IX
David Melgaard, Region IV
Stan Meiberg, Region IV
Joe Hall, OW
Gene Meier, GMP
Larry Merrill, Region III
Mari Nord, Region V
Jack Paar, NERL
David Peck, ORD
Hilary Snook, Region I
Leanne Stahl, OST
Mark Stead, Region VI
Diane Switzer,  Region I
John Macauley, ORD
Steve Paulsen, ORD
                                   Southeast Region
         JaySauber, NC-DNR
         Dave Chestnut, SC DHEC
         David Graves, SC DHEC
         Julia LightnerLDWF
         Chris Piehler, LDEQ
         George Guillen at UHCL
         Chris Kolbe of TCEQ
         Fred Leslie, ADEM
         Mark Ornelas, ADEM
Bob VanDolah, SC DHEC
Jeremy Smith, GA DNR
Dominic Guadagnoli, GA DNR
                                Gulf of Mexico Region
Joie Horn, ADEM
Gail Sloan, FL DEP
Paul Carlson, FWC
Henry Folmar, MS DEQ
David  Barnes, MS DEQ
Alice Dosset, MS DEQ

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         Christian Krahforst, MA-CZM
         Phil Trowbridge, NH-DES
         Christine Olsen, CT-DEP
         Charles deQuillfeldt, NYSDEC
         Bob Connell, NJ-DEP
         Ed Santoro, DRBC
         Bob Schuster, NJDEP
         Alan Everett, PA-DEP
         Brian Anderson, DC Davis
         Larry Cooper, SCCWRP
         Rusty Fairey, MLML
         Cassandra Roberts, MLML
         Bruce Thompson, SFEI
         Steve Weisberg, SCCWRP
         Val Connor, SWRCB
         Karen Larsen, SWRCB
         Shelly Moore, SCCWRP
         Jay Davis, SFEI
         Paul Anderson (OEPA)
         Brent Kuenzli (OEPA)
         Paul Garrison (WDNR)
         Joe Marencik (IEPA)
Northeast Region
             Cathy Wazniak, MD-DNR
             Ben Anderson, DE-DNREC
             Rick Hoffman, VA-DEQ
             Mark Richards, VA-DEQ
             Don Smith, VA-DEQ
             Chris Deacutis, RI-DEM
             Dave Courtemanch, ME-DEP
                                     West Region
             Sarah Lowe, SFEI
             Greg Pettit, OR-DEQ
             Mark Bautista, OR-DEQ
             Aaron Borisenko, OR-DEQ
             Larry Caton, OR-DE
             Casey Clishe, WA-Dept. Ecol.
             Maggie Dutch, WA-Dept. Ecol.
             Ken Dzinbal, WA-Dept. Ecol.
             Valerie Partridge, WA-Dept. Ecol.
             Suzan Pool, WA-Dept. Ecol.
                                     Great Lakes
             Dawn Roush (MDNRE)
             Bob Avery (MDNRE)
             Miel Barman (WDNR)
         Robert Brock, Univ. HW
                                    Hawaii Region
                                 National Contractors
         Jennifer Linder, Tetra Tech
         Michael T. Barbour, PhD, Tetra Tech
         John O'Donnell, Tetra Tech
         Chris Turner, GLEC
         Mailee Carton, GLEC
         Dennis J. McCauley, GLEC
         Phil Monaco, Dynamac
         Marlys Cappaert, Computer Sciences
         Corporation
             MikeArbaugh, Microbac
             Laboratories
             Laura Blake, The Cadmus Group
             Alex Long, IIRMES
             Rich Gossett, IIRMES
             Shanda McGraw, EcoAnalysts
             Gary Lester, EcoAnalysts
             Betsy Bicknell, ERG

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                 1.     PROJECT PLANNING AND MANAGEMENT
1.1.    Introduction

Several recent reports have identified the need for improved water quality monitoring and
analysis at multiple scales. In 2000, the General Accounting Office (USGAO 2000) reported that
EPA, states, and tribes collectively cannot make statistically valid inferences about water quality
(via 305[b] reporting) and lack data to support key management decisions. In 2001, the National
Research Council  (NRC 2000) recommended EPA, states,  and tribes promote a uniform,
consistent approach to ambient monitoring and data collection to support core water quality
programs. In 2002, the H. John Heinz III Center for Science, Economics, and the Environment
(Heinz Center 2002) found there is inadequate data for national  reporting on fresh water,
coastal and ocean water quality indicators. The National Association of Public Administrators
(NAPA 2002) stated that improved water quality monitoring  is  necessary to help states and
tribes make more effective use of limited resources. EPA's Report on the Environment 2003
(USEPA 2003) said that there is not sufficient information to provide a national answer, with
confidence and scientific credibility, to the  question, 'What is the condition of U.S. waters and
watersheds?'

In response to this need, the U.S. EPA Office of Water, in partnership with states and  tribes, has
begun a program to assess the condition of the nation's waters via a statistically valid  approach.
The current survey, the NCCA, builds upon the previous NCA surveys including

   -»  National Coastal Assessment: Field Operations Manual (USEPA 2001B).

   -»  Coastal 2000 - Northeast Component: Field Operations Manual (Strobel 2000).

   -»  Environmental Monitoring and Assessment Program (http://www.epa.gov/emap/)

   -»  National Coastal Assessment Quality Assurance Project Plan 2001-2004 (USEPA
       2001 A).

   -»  National Coastal Condition Report  III.  (USEPA 2008)

   -»  National Coastal Condition Report  II. (USEPA 2004A).

   -»  National Coastal Condition Report. (USEPA  2001C)


The NCCA effort will provide important information to states and the public about the condition
of the nation's coastal and estuarine  resource and key stressors on a national and regional
scale.

In 2000, the NCA initiated the first in  a series of NCA Surveys. It was organized and managed
by the U.S. EPA National Health and Environmental Effects  Research Laboratory's Gulf Ecology
Division in Gulf Breeze, FL. Since then, the Oceans and Coastal Protection Division,
Washington, D.C. has assumed the role of implementing and  managing the assessment
program under the NCCA, which is now part of the overall National Aquatic Resource  Survey
project.

EPA developed this QAPP to guide the overall project and to support the states' and tribes'
participating in the NCCA. The plan contains elements of the overall project management,  data

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quality objectives, measurement and data acquisition, and information management for the
NCCA. EPA recognizes that states and tribes may have added elements, such as supplemental
indicators, that are not covered in the scope of this integrated QAPP. EPA expects that any
supplemental elements are  addressed by the states and tribes  or their designee in a separate
approved QAPP or an addendum to this QAPP. Through this survey, states and tribes have the
opportunity to collect data which can be used to supplement their existing monitoring programs
or to begin development of new programs.

The goal of the NCCA is to address two key questions about the quality of the Nation's coastal
waters:

   •   What percent of the  Nation's coastal waters are in good, fair, and poor condition for  key
       indicators of water quality, ecological  health, and recreation?
   •   What is the relative importance of key stressors such as nutrients and pathogens?

Indicators for the 2010 survey will basically remain the same as those used in the historic
National Coastal  Report, with a few modifications. The most prominent change in this year's
survey is the inclusion of coasts along the Great Lakes.  Therefore both sample collection
methods and laboratory methods will reflect freshwater and saltwater matrices.

A NCCA workgroup comprised of EPA and State partners decided on a few improvements to
the original indicators based on recommendations from a state  workshop held in 2008.  The
additions are measuring enterococcus levels as a human health indicator;  and  requiring the
measurement of photosynthetically active radiation (PAR) using instrumentation to help
standardize and improve the accuracy of the water clarity indicator. Modifications include
sediment toxicity testing using Eohaustorius or Leptochirus instead of Ampelisca sp. for saline
sites and Hyalella for freshwater sites; and ecological fish tissue studies will be conducted using
whole fish.  Finally, fish community structure, Total Suspended Solids (TSS) in water column,
and Polycyclic Aromatic Hydrocarbons (PAHs) in fish tissue will no longer be included.

Other EPA programs are conducting special  studies under the  NCCA in the Great Lakes only:
the Great Lakes Human Health Fish Tissue Study and the Great Lakes Embayment
Enhancement Study. The Office of Science and Technology (OST) within  OW is conducting the
human health fish tissue study in the Great Lakes in partnership with the Great Lakes National
Program Office. A brief description of the study is provided in Section 5.5.1. ORD's National
Health and  Ecological Effects  Research Laboratory in Duluth, MN is conducting the enhanced
assessment of  Great Lakes embayments. This study adds additional sites to the overall
selection of sites within the Great Lakes, but is otherwise following procedures as outlined in the
QAPP and other  NCCA documents.  See section 1.3 on study design for more information.

1.2.    National Coastal Condition Assessment Project Organization

The U.S. EPA's NCCA is managed through the EPA's Office of Water, Office of Wetlands,
Oceans and Watersheds (OWOW), and the director of Oceans and Coastal Protection Division
(OCPD).

Planning and implementation of the NCCA is the  responsibility  of the NCCA Survey Team which
is made up of representatives from the Office of Water, EPA-ORD, EPA-Region Offices, and
officials from state organizations.

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U.S. coastal resources will be organized into six geographical components for reporting
purposes based on past NCA reports. These are:

              West Region                CA, OR, and WA
              Northeast Region            ME, NH, MA, Rl, CT, NY, NJ, DE, MD, PA and VA
              Southeast Region           NC, SC, Atlantic coast of FL and GA
              Gulf of Mexico Region        Gulf portion of FL, AL,  MS, LA, and TX
              Hawaii Region               HI
              Great Lakes                 IL, IN, Ml, MN, OH, NY, PA.WI

The responsibilities and accountability of the various principals and cooperators are described
here and illustrated in Figure 1-1. The overall coordination of the project will be done by EPA's
Office of Water (OW) in Washington, DC, with support from the Western Ecological Division
(WED) of the Office of Research and Development (ORD) in Corvallis, Oregon and the Gulf
Ecology Division (GED) of ORD in Gulf Breeze, Florida.  Each EPA Regional  Office has
identified a Regional EPA Coordinator who is part of the EPA team providing a critical link with
state and tribal partners.  Cooperators will work with  their Regional EPA Coordinator to address
any technical issues. A comprehensive quality assurance (QA) program has been established
to ensure data integrity and  provide support for the reliable interpretation of the findings from
this project.  Technical Expert Workgroups will be convened to decide on the best and most
appropriate approaches for key technical issues, such as: (1) the selection and establishment of
thresholds for characterizing ecological condition; (2) selection and calibration of ecological
endpoints and  attributes of the biota and their relationship to stressor indicators; (3) a data
analysis plan for interpreting the data and (4) a framework for the reporting of the condition
assessment and conveying the information on the ecological status of the Nation's coasts. For
select indicators, an indicator lead may also be appointed (e.g., fish tissue)

Contractor support is provided for all aspects of this project. Contractors will provide  support
ranging from implementing the survey, sampling and laboratory processing, data management,
data analysis, and report writing.  Cooperators will interact with their Regional  EPA Coordinator
and the EPA Project Leads regarding contractual services.

The primary responsibilities  of the principals  and cooperators are as follows:

EPA Project Leader (Lead) - Gregory Colianni

    •   Provides overall coordination of the project and makes  decisions regarding the proper
       functioning of all aspects of the project; and
    •   Makes assignments  and delegates authority,  as needed, to other parts of the project
       organization.

Alternate EPA  Project Leaders- Treda Grayson, John Macauley

    •   Assists EPA  Project  Leader with coordination and assumes responsibility for certain
       aspects of the project, as agreed upon with the EPA Project Leader;
    •   Serves as primary point-of-contact for project coordination in the absence or
       unavailability of EPA Project Leader;  and
    •   Serves on the Technical Experts Workgroup and interacts with Project Leader on
       technical, logistical, and organizational issues on a regular basis.

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Regional EPA Coordinators (see list below)
   •   Assists EPA Project Leads with regional coordination activities;
   •   Serves on the Technical Experts Workgroup and interacts with Project Leads on
       technical, logistical, and organizational issues on a regular basis; and
   •   Serves as primary point-of-contact for the Cooperators.

Technical Experts Workgroup(s) - States,  EPA, academics, other federal agencies

   •   Provides expert consultation on key technical issues as identified by the EPA
       Coordination team and works with  Project Leads to resolve approaches and strategies to
       enable data analysis and interpretation to be scientifically valid.

Logistical Oversight:  GLEC -  Dennis McCauley

   •   Functions to support implementation of the project based on technical guidance
       established by the EPA Project Leads;
   •   Primary responsibility is to ensure all aspects of the project, i.e.,  technical, logistical,
       organizational, etc., are operating as smoothly as possible; and
   •   Serves as point-of-contact for questions from field crews and cooperators for all
       activities.

Cooperator(s)

   •   Under the scope of their assistance agreements, plans and executes their individual
       studies as part of the cross jurisdictional NCCA, and adheres to  all QA requirements and
       standard operating procedures (SOPs); and
   •   Interacts with the Grant Coordinator and Project Leads regarding technical, logistical,
       and organizational issues.

Field Sampling Crew Leader (as established for each cooperator or contractor crew)

   •   Functions as the senior member of each Cooperator's field sampling crew and the point
       of contact for the Field Logistics Coordinator; and
   •   Responsible for overseeing all activities of the field sampling crew and ensuring that the
       Project field method protocols are followed during all sampling activities.

Sample Kit Coordinator - Mailee Garton, GLEC

   •   Functions to support field crews by providing initial base kits to each crew and sampling
       kits, upon request, throughout the field season.

Field Logistics Coordinators: Jennifer Pitt, Tetra Tech and Chris Turner, GLEC

   •   Functions to support implementation of the project based on technical guidance
       established by the EPA Project Leads;
   •   Serves as point-of-contact for questions from field crews and cooperators for all
       activities; and
   •   Tracks progress of field sampling activities.

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Information Management Coordinator - Marlys Cappaert, CSC

   •   Functions to support implementation of the project based on technical guidance
       established by the EPA Project Leader and Alternate EPA Project Leader;
   •   Oversees all sample shipments and receives data forms from the Cooperators; and
   •   Oversees all aspects of data entry and data management for the project.

EPA QA Officer - Charles Spooner

   •   Functions as the primary officer overseeing all QA and quality control (QC) activities;
       and
   •   Responsible for ensuring that the QA program is implemented thoroughly and
       adequately to document the performance of all activities.

EPA QA Project Officer(s) - Joe Hall

   •   Oversees the transfer of samples and related records for each indicator;
   •   Ensures the validity of data for each indicator;
   •   Oversee(s) individual studies of cooperators (assistance recipients);
   •   Interacts with EPA Project Leader and Alternate EPA Project Leader on issues related to
       sampling design, project plan, and schedules for conduct of activities;
   •   Collects copies of all official field forms, field evaluation checklists and reports; and
   •   Oversees and maintains records on field evaluation visits, but is not a  part of any one
       sampling team.

QA Audit Coordinator - Maria Smith, EPA

   •   The EPA employee who will supervise the implementation of the QA audit program; and
   •   Directs the field and laboratory audits and ensures the field and lab auditors are
       adequately trained to correct errors immediately to avoid erroneous data and the
       eventual discarding of information from the assessment.

Human Health Fish Tissue  Indicator Lead - Leanne Stahl, EPA
   •   The EPA Employee who will coordinate implementation of the human  health fish tissue
       effort on the Great Lakes;
   •   Interacts with the EPA Project Leads, EPA regional  coordinators,  contractors and
       cooperators to provide information and respond to questions related to the human health
       fish tissue indicator; and
   •   Responsible for lab analysis phase of the project.

Great Lakes Embayment Enhancement Coordinator - Jack Kelly, EPA

   •   The EPA Employee who will coordinate the embayment enhancement component of the
       Great Lakes NCCA; and
   •   Interacts with the EPA Project Leads, EPA regional  coordinators,  contractors and
       cooperators to provide information and respond to questions related to embayment
       enhancement effort.

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Great Lakes Environmental Center QA Officer - Jennifer Hansen

   •   The contractor QA Officer who will supervise the implementation of the QA program; and
       Directs the field and laboratory audits and ensures the field and lab auditors are
       adequately trained to correct errors immediately to avoid erroneous data and the
       eventual discarding of information from the assessment.

Tetra Tech QA Officer - John O'Donnell

   •   Provides support to the GLEC QA Officer in carrying out the QC checks and
       documenting the quality of the activities and adherence to specified procedures.

Dynamac c/o US EPA
       Oversees analysis of nutrients, grain size and total organic carbon (TOC) samples; and
       Ensures the validity of data for each indicator.
NERL- US EPA New England Lab
       Oversees analysis of enterococcus samples.
       Ensures the validity of data for each indicator.
Tetra Tech Laboratory
       Provides analytical support for some sediment toxicity samples; and
       Ensures the validity of data for each indicator.
GLEC Laboratory
       Provides analytical support for some sediment toxicity samples; and
       Ensures the validity of data for each indicator.
Cadmus
       Subcontracts analysis of benthic macroinvertebrate samples and metals and organic
       chemistry on both eco-fish and sediment samples; and
       Ensures the validity of data for each indicator.
IIRMES
       Provides analytical support for sediment and fish tissue chemistry samples; and
       Ensures the validity of data for each indicator.
Eco Analysts
       Oversees analysis of macroinvertebrates; and
       Ensures the validity of data for each indicator.
Microbac Laboratories

   •   Acts as a holding facility for human health fish tissue samples.

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Table 1.2-1 Contact List.
                   Contractors and National Laboratory Contacts
Information Management Coordinator
Marlys Cappaert
Computer Sciences Corporation
200 S.W. 35th Street
Corvallis, OR 97333
(541) 754-4467
(541)754-4799 fax
cappaert.marlvs@epa.gov

Field Logistics Coordinator
Chris Turner
Great Lakes Environmental Center
c/o main office
739 Hastings St.
Traverse City, Ml 49686
(715) 829-3737
cjturner@wwt.net

Michael T. Barbour, PhD
TetraTech,  Inc.
400 Red Brook Blvd, Suite 200
Owings Mills, MD21117
410-356-8993
M ichael. Barbour@tetratech. com

Environmental Quality Assurance Chemist
John O'Donnell
TetraTech,  Inc.
10306 Eaton Place, Suite 340
Fairfax, VA 22030-2201
703-385-6000X121
703-385-6007
John.odennell@tetratech-ffx.com

David Peck
Dynamac c/o US EPA
1350 Goodnight Ave.
Corvallis, OR  97333
541-754-4426
Peck.david@epa.gov

Sarah Spotts
The Cadmus Group
617-673-7149
sarah.spotts@cadmusgroup.com
Field Logistics Coordinator
Jennifer Under
TetraTech, Inc.
400 Red Brook Blvd, Suite 200
Owings Mills, MD21117
410-356-8993
Michael.Barbour@tetratech.com
Sample Kit Coordinator
Mailee Garton
Great Lakes Environmental Center
739 Hastings St.
Traverse City, Ml 49686
(231) 941-2230
mgarton@glec.com
Dennis J. McCauley
Great Lakes Environmental Center
739 Hastings St.
Traverse City, Ml 49686
231/941-2230
dmccauley@glec.com

Jack Paar
NERL-US EPA New England Lab
11 Technology Dr.
North Chelmsford, MA 01863
617-918-8604
Paar.jack@epa.gov
Laura Blake
The Cadmus Group
617-673-7148
laura.blake@cadmusgroup.com
Alex Long
IIRMES
310-408-2985
along56@gmail.com

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Rich Gossett
IIRMES-Micro 108
CSULB Receiving Dept
1250BellflowerBlvd
Long Beach, CA 90840
310-420-4964
rgossett@csulb.edu or
richgossett@yahoo.com

Gary Lester
EcoAnalysts
208-882-2588, ext. 21
glester@ecoanalysts.com
Betsy Bicknell
Eastern Research Group
703-633-1612
betsy.bicknell@erg.com
Shanda McGraw
EcoAnalysts
1420 S. Elaine Street, Suite 14
Moscow, ID 83843
208-882-2588, ext. 30
smcgraw@ecoanalysts.com
Mike Arbaugh
Microbac Laboratories
Gascoyne Division
2101 Van Deman Street
Baltimore, MD 21224
401-633-1800
             US EPA Headquarters/Office of Research and Development
Greg Colianni
USEPA Office of Water
Office of Wetlands, Oceans and Watersheds
1200 Pennsylvania Avenue, NW(4503T)
Washington, D.C. 20460-0001
(202) 566-1249
colianni.gregory@epa.gov

Joe Hall
USEPA Headquarters
Ariel Rios Building
1200 Pennsylvania Avenue, N. W.
Washington, DC 20460
202-566-1241
hall.ioe@epa.gov

Sarah Lehmann
USEPA Office of Wetlands, Oceans and
Watersheds
1200 Pennsylvania Avenue, NW(4503T)
Washington DC 20460
202-566-1379
lehmann.sarah@epa.gov
Treda Grayson
USEPA Office of Water
Office of Wetlands, Oceans and Watersheds
1200 Pennsylvania Avenue, NW(4503T)
Washington DC 20460
(202) 566-0916
grayson.treda@epa.gov

Linda Harwell
USEPA Office of Research &
Development/NHEERL/GED
1 Sabine Island Drive
Gulf Breeze FL 32561
850-934-2464
harwell.linda@epa.gov

John Maccauley,
USEPA Office of Research &
Development/NHEERL/GED
1 Sabine Island Drive
Gulf Breeze FL 32561
850-934-9353
macauley.john @epa.gov

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Steven G. Paulsen, Ph.D.
Aquatic Monitoring and Assessment Branch
Western Ecology Division, NHEERL, ORD,
EPA 200 S.W. 35th St.
Corvallis, OR 97330
541-754-4428
Paulsen.Steve@epa.gov

Leanne Stahl
USEPA Office of Science and Technology
1200 Pennsylvania Avenue, N. W. (4305T)
Washington, DC 20460
202-566-0404
stahl.leanne@epa.gov
Maria Smith
USEPA Headquarters
Ariel Rios Building
1200 Pennsylvania Avenue, N. W.
Washington, DC 20460
202-566-1047
smith.marla@epa.gov
                         U.S. EPA Regional Coordinators
USEPA Region 1
Tom Faber
USEPA Region 1 - New England Regional
Laboratory
11 Technology Drive
North Chelmsford, MA 01863-2431
(617)918-8672
faber.tom@epa.gov

USEPA Region 2
Darvene Adams
USEPA Facilities
Raritan Depot
2890 Woodbridge Avenue
Edison, NJ 08837-3679
(732) 321-6700
adams.darvene@epa.gov

USEPA Region 3
Jack Kelly
1650 Arch Street
Philadelphia, PA 19103-2029
215-814-3112
kelly.iack@epa.gov
USEPA Region 1 - New England Regional
Laboratory
Diane Switzer
11 Technology Drive
North Chelmsford, MA 01863-2431
617-918-8377
switzer.diane@epa.gov
USEPA Region 3
Larry Merrill
USEPA Region 3
1650 Arch Street
Philadelphia, PA 19103-2029
(215)814-5452
merrill.larry@epa.gov
USEPA Region 4
Bonita Johnson
USEPA Region 4
61 Forsyth Street, S.W.
Atlanta, GA 30303-8960
(404) 562-9388
iohnson.bonita@epa.gov

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USEPA Region 4
David Melgaard
61 Forsyth Street, S.W.
Atlanta, GA 30303-8960
404-562-9265
melgaard.david@epa.gov
USEPA Region 5
Mari Nord
USEPA Region 5
77 West Jackson Boulevard
Chicago, IL 60604-3507
(312) 886-3017
nord.mari@epa.gov
USEPA Region 6
Linda Hunt
USEPA Region 6
1445 Ross Avenue
Suite 1200
Dallas, TX 75202-2733
(214)-665-9729
hunt.linda@epa.gov

USEPA Region 9
Janet Hashimoto
75 Hawthorne Street
San Francisco, CA 94105
(415)972-3452
hashimoto.ianet@epa.gov
USEPA Region 6
Mark Stead
1445 Ross Avenue
Suite 1200
Dallas, TX 75202-2733
(214)665-2271
stead .mark@epa.gov
USEPA Region 10
Gretchen Hayslip
1200 Sixth Avenue
Seattle, WA 98101
(206) 553-1685
hayslip.gretchen@epa.gov

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                                    Project Management
                           Proj e ct Le ad: Gre gory C o li anm, EPA- OW
                           Project Co-Lead:  Treda Grays on, EPA-OW
                             Project QA Lead: Joe Hall, EPA-OW
                          Technical Advisor: John Macauley/EPA-ORD
                                             OWOW QA
                                           Overs ight/Re view
                                           Charles Spooner
        Study Design
    Tony Olsen EPA-ORD
           Field Logistics
      Implementation Coordinator

              Training
     EPA OW, ORD and Regions,
             Contractors

        Field Implementation
  State.Tribal Water Quality Agencies,
    EPA ORD/Regions, Contractors

        Select Indicator Leads
HHFish Tissue - Leanne Stahl, EPA-OW/
   Pathogens - Jack Paar - EPA-ORD
GL Enhancements -  Jack Kelly, EPA-QRD
Field Pro to co Is/Indicator
       Selection
  EPA OW and ORD
     State/Tribal
  Steering Committee
                                      Sample Flow
Nutrients Lab

M acroinvertebrate
Lab

S e diment T o xicity
Lab

Ecological fish
Lab
Pathogens
Lab

Sediment Chern
Lab

Phytoplakton
Lab (GL only)
                              Information Management
                                WED/SRA - Marlys Cappaert
                                        Final D ata
                                    STORET/WQX - OW
                                               HH Fish Tissue
                                                   QAPP
                                               \eanne Stahl Leat.
                                     Assessment
                                      EPA-OW Lead
                                   EPA ORD and Regions,
                                       States, Tribes,
                                Cooperators and other partners
Figure 1.1 NCCA Project Organization.

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1.3.    Study Design

The NCCA is designed to be completed during the index period of June through the end of
September 2010. Field crews will collect a variety of measurements and samples from
predetermined sampling locations (located with an assigned set of coordinates).

With input from the states and other partners, EPA used an unequal probability design to select
682 marine sites along the coasts of the continental United States and 225 freshwater sites from
the shores of the Great Lakes. Fifty sites were drawn for Hawaii.  Field  crews will  collect a
variety of measurements and samples from predetermined sampling areas associated with an
assigned set of coordinates.  See maps of coastal sites in Figures 1-2 and 1-3.

To improve our ability to assess embayments as well as shorelines in the Great Lakes, EPA
added  150 randomly selected sites in bays and embayments across all 5 Great Lakes (sites not
included in the maps below). This intensification constitutes the Great Lakes Embayment
Enhancement. Additional sites were also identified for Puerto Rico and Alaska to provide an
equivalent design for these coastal areas if these states and territories choose to  sample them.
Additionally, related sampling will occur on reef flat (coastal areas) of American Samoa,  Guam
and the Northern Mariana Islands during the 2010 field season (not included on map below).
* X
*
;. f
*
1
^••-^•'Y.
A J y
It

Legend
• 2010 Marine Slips
US States Boundary

*
*
.'••
Hawaii

«*» .
!«.»»•• *

2010 EPA National Coastal Condition Assessment 255 510 1.020
MAO 1983 Albers Mfrtere 0 240 480 960
[^j TtTRATECH
4 .,,...,.1.. «,.,i.i CLt.AJI BOlUtl-QM*
   Figure 1.2. NCCA Marine Base Sites.

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                                                                        Legend

                                                                         •  2010  Great Lakes Sites

                                                                            US States Boundary

                                                                          H Canadian Boundary
       2010 EPA National Coastal Condition Assessment
                    NAD 1983 Am, ii'. Malnm
                    Map p(ocluom) 01-18- J010
                                                    75   ISO
                                                                 Mtnom««>    p|t] TtTRA TECH

                                                                    220
                                                                 ^^^^',\r-,       ,,,..-u,.,..
   Figure 1.3. NCCA Great Lakes Coastal Base Sites.
        1.3.1.
                    Project Schedule
Training and field sampling will be conducted in 2010. Sample processing and data analysis will
be completed by 2011 in order to publish a report the following year.
Scheduled date of training
April 6 to April 8, 2010
May 4 to May 6, 2010
May 4 to May 6, 2010
May 11 to May 13, 2010
May 18 to May 20, 2010
May 18 to May 20, 2010
May 25 to May 27, 2010
June 7 to June 11, 2010
                                       Region
                                       Training

                                       Reg 6
                                       Reg 4
                                       Reg 5
                                       Reg 5
                                       Reg 9&10
                                       Reg1
                                       Reg 3
                                       Reg 2
Webinar

Completed
Completed
Completed
Completed
Completed
Completed
Completed
Completed

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Data and Peer review:

Scheduled date                         Activity

October 2010-April 2011           Data validation
April 01, 2011                     All data transferred to EPA
May-September 2011              Data analysis workshops/meetings/calls
September 2011-February 2012    Internal peer review meetings with states, cooperators,
participants
February/March 2012              Release for external peer review1
June/July 2012                   Public review of draft

1.4.   Scope of QA  Project Plan

This QAPP addresses the data acquisition efforts of NCCA, which focuses on the 2010
sampling of coasts across the United States. Data from approximately 907 coastal sites
(selected with a probability design) located along the contiguous coastal marine and Great
Lakes states and 45 sites along the Hawaiian shoreline will provide a comprehensive
assessment of the Nation's coastal waters.  Companion documents to this QAPP that are
relevant to the overall project include:

    •   National Coastal Condition Assessment:  Field Operations Manual (EPA, 201OA)

    •   National Coastal Condition Assessment:  Laboratory Methods Manual (EPA, 201 OB)

    •   National Coastal Condition Assessment:  Site Evaluation Guidelines (EPA, 201OC)

        1.4.1.       Overview of Field Operations

Field data acquisition activities are implemented for the NCCA, based on guidance developed
by EMAP.  Funding for states and tribes to conduct field data collection activities are provided
by EPA under Section  106 of the Clean Water Act. Survey preparation is initiated with selection
of the sampling locations by the Design Team  (ORD in Corvallis).  Each site is given a unique
ID which identifies it throughout the pre-field, field, lab, analysis, and data management phases
of the project.  The list of sampling locations is distributed to the EPA Regional  Coordinators,
states, and tribes. With the sampling location list, state and tribal field crews can begin site
reconnaissance on the primary sites and alternate replacement sites and begin  work on
obtaining access permission to each site.  Specific procedures for evaluating each sampling
location and for replacing non-sampleable sites are documented in NCCA: Site  Evaluation
Guidelines (EPA, 201 OC). Each crew is responsible for procuring, as needed, scientific
collecting permits from State/Tribal and Federal agencies. The field teams will use standard
field equipment and supplies as identified in the Equipment and Supplies List  (Appendix A of the
Field Operations Manual (EPA, 201 OA)). Field Team coordinators from states and tribes will
work with Field Logistics Coordinators to coordinate equipment and supply requirements.  This
helps to ensure comparability of protocols across states.  Detailed lists of equipment required
1 The proposed peer review schedule is is contingent upon timeliness of data validation, schedule
availability for regional meetings and experts for the data analysis workshop.

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for each field protocol, as well as guidance on equipment inspection and maintenance, are
contained in the Field Operations Manual (EPA, 2010A).

Field measurements and samples are collected by trained teams. The field team leaders must
be trained at an EPA-sponsored training session. Ideally, all members of each field team
should attend one EPA-sponsored training session before the field season in their state or tribal
jurisdiction.  Field sampling audits or evaluation visits will be completed  for each field team.  The
training program stresses hands-on practice of methods, consistency among crews, collection
of high quality data and samples, and safety. Training documentation will  be maintained by the
Project QA Officers.

For each site, crews prepare a dossier that contains the following applicable information: road
maps, copies of written access permissions to boat launches, scientific collection permits,
coordinates of the coastal site, information brochures on the program for interested parties, and
local area emergency numbers. Whenever possible, field team leaders attempt to contact
owners of private marinas or boat launches (as appropriate) approximately two days before the
planned sampling date. As the design requires repeat visits to select sampling locations, it is
important for the field teams to do everything possible to maintain good  relationships with
launch owners.  This includes prior contacts, respect of special requests, closing gates, minimal
site disturbance, and removal of all materials, including trash, associated with the sampling visit.

The site verification process is shown in Figure 1-4.  Upon arrival at a site, the location is
verified by a Global Positioning System (GPS) receiver, landmark references, and/or local
residents. Samples and measurements for various parameters are collected in  a specified
order (See Section 2.1, Figures 2-1 through 2-3, of Field Operations Manual (EPA, 2010A)).
This order has been set up to minimize the impact of sampling for one parameter upon
subsequent parameters. All methods are fully documented in step-by-step procedures in the
NCCA Field Operations Manual (EPA, 201OA).  The manual also contains detailed instructions
for completing documentation, labeling samples, any field processing requirements, and sample
storage and shipping.  Field communications will be through Field Logistics Coordinators (see
Table 1.2.1), and may involve regularly scheduled conference calls or contacts.

Standardized field data forms (see Appendix B,  NCCA Field Operations Manual (EPA, 201 OA))
are the primary means of data recording. On completion, the data forms are reviewed by a
person other than the person who initially entered the information. Prior to departure from the
field site, the field team leader reviews all forms and labels for completeness and legibility and
ensures that all samples are properly labeled and packed.

Upon return from field sampling to the office, completed data forms are sent to the Information
Management Coordinator in Corvallis, Oregon for entry into a computerized data base.  Forms
are to be sent within 2 weeks of sample collection.  The Information Management Coordinator
will ensure that electronic data files are reviewed independently to verify that values are
consistent with those recorded on the field data form or original field data file.

Samples are stored or packaged for shipment in accordance with instructions contained in the
Field Operations Manual (EPA, 201 OA). Precautions are taken so holding times are not
exceeded.  Samples which must be shipped are delivered to a commercial carrier; copies of
bills of lading or other documentation are maintained by the team.  The Information
Management Coordinator is notified to track the sample shipment; thus, tracing  procedures can
be initiated quickly in the event samples are not received.  Chain-of-custody forms are
completed for all transfers of samples, with copies maintained by the field team.

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The field operations phase is completed with collection of all samples or expiration of the
sampling window.  Following the field seasons, debriefings will be held which cover all aspects
of the field program and solicit suggestions for improvements.
    Locate X-site on map
     Conduct preliminary
        evaluation
      (desktop / office)
                                             Regional
                                           NCCA rep and
                                           Coastal Team
                                           Leader confirm
                                           sites should be
                                             dropped''
Is X-site in a
  coastal
 nearshore
  area?
                                         Permission to access
                                         granted (as needed)
                                                                                   Select alternate Site
          Yes / Maybe
1

X-site Verification
(on-site)
       Complete site
    verification form and
       submit to ....
       Sample X-site
                                                                              (Complete site
                                                                           verification form and
                                                                              submit to ....
                                                                                   Identify reason(s) why
                                                                                   site not sampleable
                                            Can X-site be
                                            moved within a
                                            .02 nm area to
                                              achieve
                                            sampleability?
         Figure 1.4. Site Evaluation Diagram.

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        1.4.2.       Overview of Laboratory Operations

National Laboratories:
 Because some states may not be adequately equipped and staffed to conduct certain highly
 specialized analyses related to several of the core NCCA indicators, and/or the cost to contact
 analyses for a limited number of samples may be prohibitive, the U.S. EPA will designate
 several "National Laboratories" to conduct these analyses for any state which so elects, at a
 nominal cost per sample. This approach would also ensure data uniformity between the
 participating states. National Laboratories have been selected for the following core activities:

   •   analytical chemistry (organic and metal contaminants in both sediment and fish tissue
       matrices);

   •   benthic community structure;

   •   nutrient analyses;

   •   sediment toxicity testing; and

   •   pathogen indicators.


The designated National Laboratories must comply with the QA/QC requirements described in
this document.

In-State Laboratory Analyses:

For any analyses other than those conducted through the above National Laboratories,  each of
the states participating in NCCA will be responsible for the arrangements to analyze the field
samples that they collect. These agreements will be negotiated by the individual states, not
through the EPA. Some analyses may be conducted in-house by state agency laboratories or
universities, while others are contracted out to private laboratories or other  states. However,
any laboratory selected to conduct analyses with NCCA samples must demonstrate that they
can meet the quality standards  presented in this QAPP and the NCCA  Laboratory Methods
Manual (EPA, 201 OB) and NCCA Field Operations Manual (EPA, 201OA).  Later sections will
address initial demonstrations of technical capability and performance evaluations.

All laboratories providing analytical support to NCCA must adhere to the provisions of this
integrated QAPP.  Laboratories will provide information documenting their ability to conduct the
analyses with the required level of data quality before analyses begin.  The documentation will
be sent to Joe Hall at EPA Headquarters. Such information might include results from
interlaboratory comparison studies, analysis of performance evaluation samples, control charts
and results of internal QC sample or internal reference sample analyses to  document achieved
precision, bias, accuracy, and method detection limits. Contracted laboratories will be required
to provide copies of their Data Management Plan.  Laboratory operations may be evaluated  by
technical systems audits, performance evaluation studies,  and by participation in interlaboratory
sample exchange.  All analytical laboratories should follow best laboratory  practices.

In the performance-based QA approach for analytical chemistry, no set method is required of
the laboratory as long as the laboratory continues to meet the quality standards of the
program. Samples should be processed and analyzed as designated batches consisting of 25

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or less samples and each batch will include prescribed QC samples (e.g., reagent blanks,
matrix spikes and matrix spike duplicates, and standard reference materials (SRMs)). These
QC samples represent the basic elements that provide estimates of accuracy and precision for
the analyses of chemical contaminants. The overall analytical process involves several
additional QC- related components or checks (e.g., calibration curves, use of internal
standards, and control charts). When these QC checks are embedded in each batch, the
analyst should be able to quickly assess the overall data quality on a per batch basis and take
corrective measures if there are deficiencies. If data for a class of compounds consistently
fails any of the NCCA quality standards, the laboratory management must notify the State QA
Coordinator of the problem and seek recommended corrective actions prior to submitting the
final data report.

As noted above, before a laboratory is authorized to analyze actual field collected samples,
the lab must provide documentation to demonstrate its technical capability to  perform at the
level required by NCCA.  Laboratories that have successfully participated in a program
such as the NIST/NRCC/ NOAA/EPA Intercomparison Exercises in the last 5 years may
submit their recent results to Joe Hall, the NCCA QA Project Manager, for evaluation.  For
labs that  have not undertaken this exercise, the following steps may be required.

Labs should calculate and submit method detection limits (MDLs) for each analyte of interest for
the each  matrix which they plan to analyze. Each laboratory is required to follow the procedure
specified in 40 CFR Part 136 (Federal Register, Oct. 28, 1984) to calculate MDLs for each
analytical method employed. To indicate the level of detection required, target MDLs have been
established (Section 5.3, Table 5.3-2 and Section 5.5, Table 5.5-10) and the MDLs reported by
candidate laboratories should be equal to or less than the target values. It is important that a
laboratory establishes, up front, its  capability to generally meet the MDL requirements; this is a
key factor that must be established before proceeding further with the performance evaluation
(PE).

Once the MDL requirements are met for an analyte class and matrix type, the laboratory may
be issued a PE sample to analyze.  The PE sample will be provided by the NCCA team or
contractors. When available, SRMs or Certified Reference Material (CRMs) should be used in
these exercises. The basic quality criteria for these PE exercise are that the laboratory results
generally meet accuracy goals set by NCCA. For the organic analysis, the general goal for
accuracy is laboratory agreement within ± 35% of the certified or "true value" for the analytes of
interest; for inorganic analysis, laboratory agreement within ± 20% of the accepted true value.
These requirements apply only to those analytes with certified values >10 times the
laboratory's calculated MDL. The participating laboratory will submit the results of their
completed PE exercises to the the  NCCA QA Project Manager, Joe Hall, to be evaluated.

Below is a brief summary of the NCCA laboratory indicators:  laboratory must meet the
minimum quality criteria set forth. See Sections 2 and 5 for a full discussion of the quality
criteria that govern these analytical chemistry procedures in addition to the  NCCA Lab
Operations manual.

Water Quality Indicators

Conditions of water quality will be evaluated for each NCCA site through the analyses  of
indicators of anthropogenic enrichment, including nutrient levels, chlorophyll a content,
phytoplankton community and pathogen indicator.  Samples for these indicators will be obtained
by using  both filtered and unfiltered site water. Field crews will retain the material filtered out for

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the analyses of chlorophyll a for the lab analyses of soluble nutrients. Laboratory methods will
be performance based but suggested methods can be found in theNCCA Laboratory Methods
Manual (EPA, 201 OB) and EPA methods can be found at
http://www.epa.gov/waterscience/methods/. Preferred methods are as follows:

   •   chlorophyll a analysis - acetone extraction, fluorometric analysis

   •   soluble nutrients - spectrophotometry (autoanalyzer)

   •   phytoplankton - identification and enumeration

   •   enterococcus - Quantitative Polymerase Chain Reaction (qPCR)


Appropriate QC samples (e.g., standards, reagent blanks, duplicates, and standard reference
materials) will be run with each batch of samples. If the prescribed quality criteria are not
consistently met, the analyst will confer with the laboratory supervisor for corrective measures
before proceeding with additional samples.

Sediment Silt-Clay Content Determination

Silt-clay will be determined for sediment collected from each station by the differentiation of
whole sediment into two fractions: that which passes through a 63-um sieve (silt-clay), and that
which is retained on the screen (sands/gravel). The results will be expressed as percent silt-
clay. The procedures to be used should be based on those developed for EMAP-E and
described in the NCCA Laboratory Operations Manual.

TOC

Analysis of sediment TOC will  be conducted with sediment sampled from each NCCA Site. The
sediment will be dried and acidified to remove sources of inorganic carbon (e.g. carbonates);
the analysis will be conducted  using a TOC analyzer to combust the sample to form CO2 which
is measured by infrared detection  (U.S. EPA, 1995).

Macrobenthic Community Assessments

Macrobenthic organisms collected and preserved at each NCCA site will be sorted and
identified at the laboratory typically to the lowest practicable level. The sample will first be
sorted into major taxon groups which then will  be further identified to species and counted. A
senior taxonomist will oversee and periodically review the work performed by technicians.  Refer
to the NCCA Laboratory Operations Manual for additional information on the method.

Sediment Toxicity Testing

At each NCCA site, surficial sediment will be collected for use in acute toxicity tests in which
marine or freshwater amphipods (depending on whether the site is marine or Great Lake) will be
exposed to test treatments of sediment for up to 10 days under static conditions; the tests will
be aerated. The toxicity tests will be conducted in accord to the standard method described in
the NCCA Laboratory Operations  Manual; these protocols are based on American  Society for
Testing and Materials (ASTM)  Standard Method E-1367-90 (ASTM, 1991). After 10 days
exposure, the surviving amphipods will be counted  and results expressed as test treatment
survival compared to control survival. These tests and will maintain a flexible policy regarding
what species to permit as test organisms.

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Sediment and Fish Tissue Chemical Contaminant Testing

Sediment samples collected at each NCCA site will be tested for the presence of a variety of
chemical contaminants. For metals, microwave digestion will be followed by inductively coupled
plasma (ICP) analysis. Mercury samples will be digested and analyzed using the cold vapor
technique.  Polychlorinated biphenols (PCB), organochlorine pesticide and
dichlorodiphenyltrichloroethane (DDT) metabolite extracts will be analyzed by gas
chromatograph/electron capture detector (GC/ECD) or gas chromatograph/electrolytic
conductivity detector (GC/ELCD).  A gas chromatograph/mass spectrophotometer (GC/MS) will
be used to analyze samples for PAHs.

        1.4.3.       Data Analysis and Reporting

A technical  workgroup convened by the EPA Project Leader is responsible for development of
a data analysis plan that includes a verification and validation strategy.  These processes are
summarized in the indicator-specific sections of this QAPP. Validated data are transferred to
the central data base managed by EMAP information  management support staff located at
WED in Corvallis.  Information management activities are discussed further in Section 4. Data
in the WED data base are available to Cooperators for use in development of indicator
metrics.  All validated measurement and indicator data from the NCCA are eventually
transferred  to EPA's Water Quality Exchange (WQX) for storage in EPA's STORET
warehouse  for public accessibility.  The Data Analysis plan is described in Section 7 of this
QAPP.

        1.4.4.       Peer Review

The Survey will undergo a thorough peer review process, where the scientific community and
the public will be given the opportunity to provide comments. Cooperators have been actively
involved in the development of the overall project management, design, methods, and
standards including the drafting of four key project documents:

   •  National Coastal Condition Assessment: Quality Assurance Project Plan (EPA 841-R-
      09-004)

   •  National Coastal Condition Assessment: Field Operations Manual (EPA, 201OA)

   •  National Coastal Condition Assessment: Laboratory Methods Manual (EPA, 201 OB)

   •  National Coastal Condition Assessment: Site  Evaluation Guidelines (EPA, 201OC)


Outside scientific experts from universities, research centers, and other federal agencies have
been instrumental in indicator development and will continue to play an important role in data
analysis.

The EPA will utilize a three tiered approach for peer review of the Survey: (1) internal and
external review by EPA, states, other Cooperators and partners, (2) external scientific peer
review, and (3) public review.

Once data analysis has been completed, Cooperators will examine the results at regional
meetings. Comments and feedback from the Cooperators will be incorporated into the draft
report. Public and scientific peer review will occur  simultaneously. This public comment period

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is important to the process and will allow EPA to garner a broader perspective in examining
the results before the final report is completed. The public peer review is consistent with the
Agency and OMB's revised requirements for peer review.

Below are the proposed measures EPA will implement for engaging in the peer review
process:

    1.  Develop and maintain a public website with links to standard operating procedures,
       quality assurance documents, fact sheets, cooperator feedback, and final report;

    2.  Conduct technical workgroup meetings composed of scientific experts, cooperators,
       and EPA to evaluate and recommend data analysis options and indicators;

    3.  Hold national meeting where cooperators will provide input and guidance on data
       presentation and an approach for data analysis;

    4.  Complete data validation on all chemical,  physical and biological data;

    5.  Conduct final data analysis with workgroup to generate assessment results;

    6.  Engage peer review contractor to identify external peer review pane;I

    7.  Develop draft report presenting assessment results;

    8.  Conduct regional meetings with cooperators to examine and comment on results;

    9.  Develop final draft report incorporating input from cooperators and results from data
       analysis group to be distributed for peer and public review;

    10. Issue  Federal Register (FR) Notice announcing document availability  and hold
       scientific/peer review and public comment (30-45 days); and

    11. Consider scientific and public comments and produce a final report


                        2.     DATA QUALITY OBJECTIVES
It is a policy of the U.S. EPA that Data Quality Objectives (DQOs) be developed for all
environmental data collection activities following the prescribed DQO Process.  DQOs are
qualitative and quantitative statements that clarify study objectives, define the appropriate
types of data, and specify the tolerable levels of potential decision errors that will be used as
the basis for establishing the quality and quantity of data needed to support decisions (EPA
2006B).  Data quality objectives thus provide the criteria to design a sampling program within
cost and resource constraints or technology limitations imposed upon a project or study.
DQOs are typically expressed in terms of acceptable uncertainty (e.g., width of an uncertainty
band or interval) associated with a point estimate at a desired level of statistical confidence
(EPA 2006B).  The DQO Process is used to establish performance or acceptance criteria,
which serve as the basis for designing a plan for collecting data of sufficient quality and
quantity to support the goals of a study (EPA 2006B). As a general rule, performance criteria
represent the full set of specifications that are needed to design a data or information
collection effort such that, when implemented, generate newly-collected data that are of
sufficient quality and quantity to address the project's goals (EPA 2006B).  Acceptance criteria
are specifications intended to evaluate the adequacy of one or more existing  sources of
information or data as being acceptable to support the project's intended use (EPA 2006B).

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2.1.    Data Quality Objectives for the National Coastal Condition Assessment


NCCA has established target DQOs for assessing the current status of selected indicators of
condition for the conterminous U.S.coastal resources as follows:

   •   For each indicator of condition, estimate the proportion of the nation's estuaries and
       combined area of the Great Lakes in degraded condition within a  ± 5% margin of error
       and with 95% confidence.

   •   For each indicator of condition, estimate the proportion of regional estuarine resources
       (Northeast, Southeast, Gulf of Mexico, and West Coast) in degraded condition within a ±
       15% margin of error and with 95% confidence.

2.2.    Measurement Quality Objectives
 For each parameter, performance objectives (associated primarily with measurement error)
 are established for several different data quality indicators (following USEPA Guidance for
 Quality Assurance Plans EPA240/R-02/009).  Specific measurement quality objectives
 (MQOs) for each parameter are presented in Table 2-1.  The following sections define the
 data quality indicators and present approaches for evaluating them against acceptance
 criteria established for the program.

        2.2.1.       Method Detection Limits (Laboratory Reporting Level (Sensitivity))

 For chemical measurements, requirements for the MDL are typically established (see
 indicators in Section 5). The MDL is defined as the lowest level of analyte that can be
 distinguished from zero with 99 percent confidence based on a single measurement (Glaser
 et al.,  1981).  United State Geologic Survey (USGS) NWQL has developed a variant of the
 MDL called the long-term MDL (LT-MDL) to capture greater method variability (Oblinger
 Childress et al. 1999). Unlike MDL,  it is designed to incorporate more of the measurement
 variability that is typical for routine analyses in a production laboratory, such as multiple
 instruments, operators, calibrations, and sample preparation events (Oblinger Childress et al.
 1999). The LT-MDL determination ideally employs at least 24 spiked samples prepared and
 analyzed by multiple analysts on multiple instruments over a 6- to 12-month period at a
 frequency of about two samples per month (EPA 2004B). The LT-MDL uses "F-
 pseudosigma" (Fa)  in place of s, the sample standard deviation, used in the EPA MDL
 calculation. F-pseudosigma is a non-parametric measure of variability that is based on the
 interquartile range of the data (EPA 2004B). The LT-MDL may be calculated using either the
 mean  or median of a set of long-term blanks, or from long-term spiked sample results
 (depending o the analyte and specific analytical method). The LT-MDL for an individual
 analyte is calculated as:

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Equation 1 a             LT-MDL =  M +  (f
                                               0 J9,«- 1
Where M is the mean or median of blank results; n is the number of spiked sample results; and
FO is F-pseudosigma, a nonparametric estimate of variability calculated as:
Equation 1b                      p  -
                                           1.349
Where: Q3 and Q1 are the 75th percentile and 25th percentile of spiked sample results,
respectively.

LT-MDL is designed to be used in conjunction with a laboratory reporting level (LRL; Oblinger
Childress et al. 1999).  The LRL is designed to achieve a risk of <1% for both false negatives
and false positives (Oblinger Childress et al. 1999). The LRL is set as a multiple of the LT-MDL,
and is calculated as follows:

                                  LRL = 2 x LT-MDL
Therefore, multiple measurements of a sample having a true concentration at the LRL should
result in the concentration being detected and reported 99 percent of the time (Oblinger
Childress et al. 1999).

All laboratories will develop calibration curves for each batch of samples that include a
calibration standard with an analyte concentration equal to the LRL. Estimates of LRLs (and
how they are determined) are required to be submitted with  analytical  results. Analytical results
associated with LRLs that exceed the objectives are flagged as being  associated with
unacceptable LRLs. Analytical data that are below the estimated LRLs are reported, but are
flagged as being  below the LRLs.

        2.2.2.       Sampling Precision, Bias, and Accuracy

Precision and bias are estimates of random and  systematic  error in a measurement process
(Kirchmer, 1983;  Hunt  and Wilson, 1986,  USEPA 2002).  Collectively,  precision and bias
provide an estimate of the total error or uncertainty associated with an individual measurement
or set of measurements. Systematic errors are minimized by using validated methods and
standardized procedures across all laboratories.  Precision is estimated from repeated
measurements of samples. Net bias is determined from repeated measurements of solutions of
known composition, or from the analysis of samples that have been fortified by the addition of a
known quantity of analyte.  For analytes with  large ranges of expected concentrations, MQOs
for precision and  bias are established in both absolute and relative terms, following the
approach outlined in Hunt and Wilson (1986).  At lower concentrations, MQOs are specified in
absolute terms. At higher concentrations, MQOs are stated in relative terms.  The point of
transition between an absolute and relative MQO is calculated as the quotient of the absolute
objective divided  by the relative objective (expressed as a proportion,  e.g., 0.10 rather than as a
percentage, e.g., 10%).

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Precision in absolute terms is estimated as the sample standard deviation when the number of
measurements is greater than two:
Equation 1                    s =
                                       n-l
where Xj is the value of the replicate,  x is the mean of repeated sample measurements, and n is
the number of replicates. Relative precision for such measurements is estimated as the relative
standard deviation (RSD, or coefficient of variation, [CV]):

Equation 2                      RSD = — xlOO
                                      X
value for the set of measurements.here s is the sample standard deviation of the set of

measurements, and x equals the mean.

Precision based on duplicate measurements is estimated based on the range of measured
values (which equals the difference for two measurements). The relative percent difference
(RPD) is calculated as:
                                      A — B
                            RPD = \	IxlOO
Equation 3
where A is the first measured value, B is the second measured value.

For repeated measurements of samples of known composition, net bias (B) is estimated in
absolute terms as:


Equation 4                         B = lc-T
where x equals the mean value for the set of measurements, and T equals the theoretical
or target value of a performance evaluation sample. Bias in relative terms (B[%]) is
calculated as:
                                         rri
Equations
where x equals the mean value for the set of measurements, and T equals the theoretical or
target value of a performance evaluation sample.

Accuracy is estimated for some analytes from fortified or spiked samples as the percent
recovery. Percent recovery is calculated as:

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                                        C -C
Equation 6                 %recovery =       xlOO
where Cis is the measured concentration of the spiked sample, CM is the concentration of the
unspiked sample, and Cs is the concentration of the spike.

Precision and bias within each laboratory are monitored for every sample batch by the analysis
of internal QC samples. Samples associated with unacceptable QC sample results are
reviewed and re-analyzed if necessary.  Precision and bias across all laboratories will be
evaluated after analyses are completed by using the results of performance evaluation (PE)
samples sent to all laboratories (3 sets of 3 PE samples, with each set consisting of a low,
moderate, and high concentration sample of all analytes).

        2.2.3.       Taxonomic Precision and Accuracy

For the NCCA, taxonomic precision will be quantified by comparing whole-sample identifications
completed by independent taxonomists or laboratories.  Accuracy of taxonomy will be
qualitatively evaluated through specification of target hierarchical levels (e.g., family, genus, or
species); and the specification of appropriate technical taxonomic literature or other references
(e.g., identification keys, voucher specimens). To calculate taxonomic precision,  10 percent of
the samples will be randomly-selected for re-identification by an independent, outside
taxonomist or laboratory. Comparison of the results of whole sample  re-identifications will
provide a Percent Taxonomic Disagreement (PTD) calculated as:
Equation 7
                           PTD =
  1-
                                       comp
                                            pos
                                          N
x 100
where comppos is the number of agreements, and N is the total number of individuals in the
larger of the two counts. The lower the PTD, the more similar are taxonomic results and the
overall taxonomic precision is better. A MQO of 15% is recommended for taxonomic difference
(overall mean <15% is acceptable). Individual samples exceeding 15% are examined for
taxonomic areas of substantial  disagreement, and the reasons for disagreement investigated.

Sample enumeration is another component of taxonomic precision. Final specimen counts for
samples are dependent on the  taxonomist, not the rough counts obtained during the sorting
activity.  Comparison of counts is quantified by calculation of percent difference in enumeration
(PDE), calculated as:
Equation 8
       (\Lab\-Labl\\
PDE =	 x 100
       ^ Labi + Labi)
An MQO of 5% is recommended
(overall mean of <5% is acceptable) for PDE values. Individual samples exceeding 5% are
examined to determine reasons for the exceedance.

Corrective actions for samples exceeding these MQOs can include defining the taxa for which
re-identification may be necessary (potentially even by third party), for which samples (even

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outside of the 10% lot of QC samples) it is necessary, and where there may be issues of
nomenclatural or enumeration problems.

Taxonomic accuracy is evaluated by having individual specimens representative of selected
taxa identified by recognized experts. Samples will be identified using the most appropriate
technical literature that is accepted by the taxonomic discipline and reflects the accepted
nomenclature. Where necessary,  the Integrated Taxonomic Information System (ITIS,
http://www.itis.usda.gov/) will be used to verify nomenclatural validity and spelling. A reference
collection will be compiled as the samples are identified.  Specialists in several taxonomic
groups will verify selected individuals of different taxa, as determined by the NCCA workgroup.

        2.2.4.       Completeness

Completeness is defined as "a measure of the amount of data collected from a measurement
process compared to the amount that was expected to be obtained under the conditions of
measurement" (Stanley and Vener, 1985).

Completeness requirements are established and evaluated from two perspectives. First, valid
data for individual parameters must be acquired from a minimum number of sampling locations
in order to make subpopulation estimates with a specified level of confidence or sampling
precision.  The objective of this study is to complete sampling at 95% or more of the 1000 initial
sampling sites. Percent completeness is calculated as:


Equations                       %C = ^/C,xlOO


where V is the number of measurements/samples judged valid, and T is the total number of
planned measurements/samples.

Within each indicator, completeness objectives are also established for individual samples or
individual measurement variables or analytes. These objectives are estimated as the
percentage of valid data obtained versus the amount of data expected based on the number of
samples collected or number of measurements conducted.  Where necessary, supplementary
objectives for completeness are presented in  the indicator-specific sections of this QAPP.

The completeness objectives are established for each measurement per site type (e.g.,
probability sites, revisit sites, etc.).  Failure to achieve the minimum requirements for a particular
site type results in regional  population estimates having wider confidence intervals and may
impact the ability to make some subnational assessments.  Failure to achieve requirements for
repeat sampling (10% of samples collected) and revisit samples (10% of sites visited) reduces
the precision of estimates of index period and annual variance components, and may impact the
representativeness of these estimates because of possible bias in the set of measurements
obtained.

        2.2.5.       Comparability

Comparability is defined as "the confidence with which one data set can be compared to
another" (Stanley and Vener,  1985). A performance-based methods approach is being utilized
for water chemistry and chlorophyll-a analyses that defines a set of laboratory  method
performance requirements for data quality.  Following this approach, participating laboratories

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may choose which analytical methods they will use for each target analyte as long as they are
able to achieve the performance requirements as listed in the Quality Control section of each
Indicator section.  For all parameters, comparability is addressed by the use of standardized
sampling procedures and analytical methods by all sampling crews and laboratories.
Comparability of data within and among parameters is also facilitated by the implementation of
standardized quality assurance and quality control techniques and standardized performance
and acceptance criteria.  For all measurements, reporting units and format are specified,
incorporated into standardized data recording forms, and documented  in the information
management system.  Comparability is also addressed by providing results of QA sample data,
such as estimates of precision and bias, conducting methods comparison studies when
requested by the grantees and conducting interlaboratory performance evaluation studies
among state, university, and NCCA contractors.


        2.2.6.       Representativeness

Representativeness is defined as "the degree to which the data accurately and precisely
represent a characteristic of a population parameter, variation of a property,  a process
characteristic, or an operational condition" (USEPA 2002).  At one level, representativeness is
affected by problems in any or all of the other data quality indicators.

At another level, representativeness is affected by the selection of the target surface water
bodies, the location of sampling sites within that body, the time period when  samples are
collected, and the time period when samples are analyzed. The probability-based sampling
design should provide estimates of condition of surface water resource populations that are
representative of the region. The individual sampling programs defined for each indicator
attempt to address representativeness within the constraints of the response design, (which
includes when, where, and how to collect a sample at each site).  Holding time requirements for
analyses ensure analytical results are representative of conditions at the time of sampling.  Use
of duplicate (repeat) samples which are similar in composition to samples being measured
provides estimates of precision and bias that are applicable to sample  measurements.

                          3.     SITE SELECTION DESIGN

The overall sampling program for the NCCA project requires a randomized, probability-based
approach for selecting coastal  sites where sampling activities are to be conducted.  Details
regarding the specific application of the probability design to surface waters resources are
described in Paulsen et al. (1991) and Stevens (1994). The specific details for the collection of
samples associated with different indicators are described  in the indicator-specific sections of
this QAPP.

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3.1.    Probability Based Sampling Design and Site Selection

The target population for this project includes:

   •   All coastal waters of the United States from the head-of-salt to confluence with ocean
       including inland waterways and major embayments such as Florida Bay and Cape Cod
       Bay.  For the purposes of this study the head of salt is generally defined as < 0.5 psu
       (ppt) and represents the landward/upstream boundary.  The seaward boundary extends
       out to where an imaginary straight-line intersecting two land features would fully enclose
       a body of coastal water. All waters within the enclosed area are defined as estuarine,
       regardless of depth or salinity.

   •   Near shore waters of the Great Lakes of the United States and Canada.  Near shore
       zone is defined as region from shoreline to 30m depth constrained to a maximum of 5
       km from shoreline. Great Lakes include Lake Superior, Lake Michigan, Lake Huron,
       Lake Erie, and Lake Ontario. The NARS Great Lakes survey will be restricted to the
       United States portion.


         3.1.1.       Survey Design for the Marine Waters

The sample frame was derived from the prior National Coastal Assessment sample frame
developed by ORD  Gulf Breeze Ecology Division. The prior GED sample frame was
enhanced as part of the National Coastal Monitoring Network design (National Water Quality
Monitoring Network) by including information from NOAA's Coastal Assessment Framework,
boundaries of National Estuary Programs (NEP) and identification of major coastal systems.
Information on salinity zones was obtained from NOAA for the NCCA. For Delaware Bay,
Chesapeake Bay, Puget Sound and state of South Carolina, the prior NCCA sample frames
were replaced by GIS layers provided by South Carolina Department of Health &
Environmental Control, Washington Department of Ecology, Chesapeake Bay Program and
Delaware River Basin Commission, ensuring that no prior areas in NCCA were excluded and
any differences were clearly identified in the new NCCA sample frame.

A Generalized Random Tessellation Stratified (GRTS) survey design for an area resource was
used for the NCCA. The survey design is a stratified design with unequal probability of
selection based on area within each stratum.  The details are given below:

Unequal probability categories were created based  on area of polygons within each major
estuary.  The number of categories ranged from 3 to 7. The categories were used to ensure
that sites were selected in the smaller polygons. The Design includes three panels: "Revisit"
identifies sites that are to be visited twice, "Base" identifies remaining sites to be visited, and
"Over" identifies sites available to be used as replacement sites.  Over sample sites were
selected independent of the other two panels.  The expected sample size is 682 sites for
conterminous coastal states and 45 sites each for Hawaii and Puerto Rico. The maximum
number of sites for a major estuary was 46 (Chesapeake Bay). Total number of site visits is
750 allocated to 682 unique sites and  68 sites to be revisited. Additionally, over sample sites
were selected to not only provide replacement sites that either are not part of the target

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population or could not be sampled but also to accommodate those states on National Estuary
Programs who may want to increase the number of sites sampled within their state for a state-
level design or NEP design.


        3.1.2.       Survey Design for the Great Lakes

The sample frame was obtained from Jack Kelly, US EPA ORD.  A Generalized Random
Tessellation Stratified (GRTS) survey design for an area resource was used.  The survey design
is stratified  by Lake and country with unequal probability of selection based on state shoreline
length within each stratum. Unequal probability categories are states or province within each
Great Lake based on proportion of state shoreline length within each stratum.  The design uses
a single panel, "Base", with an over sample that was selected independent of the Base panel.
The expected sample size is for 45 sites in Shallow NearShore zone for each Great Lake and
country combination for a total of 405 sites.  Sample sizes were allocated proportional to
shoreline length by state within  each Great Lake.  An over sample size of 405 (100%) was
selected to  provide replacement sites that either are not part of the target population or could
not be sampled.  The over sample sites were selected independently of the base design.

        3.1.3.       Revisit Sites

Of the sites visited in the field and found to be target sites, a total of 10% will be revisited.  The
primary purpose of this revisit set of sites is to allow variance estimates that would provide
information on the extent to which the  population estimates  might vary if they were sampled  at
a different time.
                        4.     INFORMATION  MANAGEMENT
Environmental monitoring efforts that amass large quantities of information from various sources
present unique and challenging data management opportunities. To meet these challenges, the
NCCA employs a variety of well-tested information management (IM) strategies to aid in the
functional organization and ensured integrity of stored electronic data.  IM is integral to all
aspects of the NCCA from initial selection of sampling sites through the dissemination and
reporting of final, validated data. And, by extension, all participants in the NCCA have certain
responsibilities and obligations which also make them a part of the IM system. This "inclusive"
approach to managing information helps to:

   •   Strengthen relationships among NCCA participants.
   •   Increase the quality and relevancy of accumulated data.
   •   Ensure the flexibility and sustainability of the NCCA IM structure.
This IM strategy provides a congruent and scientifically meaningful approach for maintaining
environmental monitoring data that will satisfy both scientific and technological requirements of
the NCCA.

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4.1.    Roles and Responsibilities

At each point where data and information are generated, compiled, or stored, the NCCA team
must manage the information.  Thus, the IM system includes all of the data-generating activities,
all of the means of recording and storing information, and all of the processes which use data.
The IM system also includes both hardcopy and electronic means of generating, storing,
organizing and archiving data and the efforts to achieve a functional IM process is all
encompassing.  To that end, all participants in the NCCA play an integral part within the IM
system. The following table provides a summary of the IM responsibilities identified by NCCA
group.  Specific information on the field team responsibilities for tracking and sending
information is found in the Field Operations Manual (EPA, 201OA).

Table 4.1. Summary  of IM Responsibilities.
    NCCA
    Group
 Contact
 Primary Role
            Responsibility
 Field Teams
State
partners
and
contractors
Acquire in-situ
measurements
and prescribed
list of
biotic/abiotic
samples at
each site
targeted for the
survey
Complete and review field data forms and
sample tracking forms for accuracy,
completeness, and legibility.
Ship/fax field and sample tracking forms to
NCCA IM Center so information can be
integrated into the central database
Work with the NCCA IM Center staff to
develop acceptable file structures and
electronic data transfer protocols should
there be a need to transfer and integrate
data into the central database
Provide all data as specified in Field
Operations Manual (EPA, 201 OA) or as
negotiated with the NCCA Project Leader.
Maintain  open communications with NCCA
IM Center regarding any data issues
 Analytical
 Laboratories
State
partners
and
contractors
Analyze
samples
received from
field teams in
the manner
appropriate to
acquire
biotic/abiotic
indicators/mea
surements
requested.
Review all electronic data transmittal files for
completeness and accuracy (as identified in
the Quality Assurance Project Plan).
Work with the NCCA IM Center staff to
develop file structures and electronic data
transfer protocols for electronic-based data.
Submit completed sample tracking forms to
NCCA  IM Center so information can be
updated in the central database
Provide all data and metadata as specified in
the laboratory transmittal guidance section  of
the Quality Assurance Project Plan or as
negotiated with the NCCA Project Leader.

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NCCA
Group


NCCA IM
Center staff



























NCCA
Quality
Assurance
Manager







NCCA Data
Analysis
and
Reporting

Contact


USEPA
ORD
NHEERL
Western
Ecology
Division-
Corvallis






















USEPA
Office Of
Water








USEPA
Office of
Water


Primary Role


Provides
support and
guidance for all
IM operations
related to
maintaining a
central data
management
system for
NCCA.



















Review and
evaluate the
relevancy and
quality of
inform ation/dat
a collected and
generated
through the
NCCA
surveys.

Provide the
data analysis
and technical
supporting

Responsibility
• Maintain open communications with NCCA IM
Center regarding any data issues.
• Develop/update field data forms.
• Plan and implement electronic data flow and
management processes.
• Manage the centralized database and
implement related administration duties.
• Receive, scan, and conduct error checking
of field data forms.
• Monitor and track samples from field
collection, through shipment to appropriate
laboratory.
• Receive data submission packages
(analytical results and metadata) from each
laboratory.
• Run automated error checking, e.g.,
formatting differences, field edits, range
checks, logic checks, etc.
• Receive verified, validated, and final
indicator data files (including record changes
and reason for change) from QA reviewers.
Maintain history of all changes to data
records from inception through delivery to
WQX..
• Organize data in preparation for data
verification and validation analysis and public
dissemination.
• Implement backup and recovery support for
central database.
• Implement data version control as
appropriate.
• Monitor instrument and analytical quality
control information.
• Evaluate results stemming from field and
laboratory audits.
• Investigate and take corrective action, as
necessary, to mitigate any data quality
issues.
• Issue guidance to NCCA Project Leader and
IM Center staff for qualifying data when
quality standards are not met or when
protocols deviate from plan.
• Provide data integration, aggregation and
transformation support as needed for data
analysis.
• Provide supporting information necessary to

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                                                      Page 32 of 121
NCCA
Group
Team
Data
Finalization
Team
Contact

TBD
Primary Role
NCCA
reporting
requirements
Provides data
librarian
support
Responsibility
create metadata.
• Investigate and follow-up on data anomalies
identified data analysis activities.
• Produce estimates of extent and ecological
condition of the target population of the
resource.
• Provide written background information and
data analysis interpretation for report(s).
• Document in-depth data analysis procedures
used.
• Provide mapping/graphical support.
• Document formatting and version control.
• Prepare NCCA data for transfer to USEPA
public web-server(s).
• Generate data inventory catalog record
(Science Inventory Record)
• Ensure all metadata is consistent, complete,
and compliant with USEPA standards.
        4.1.1.
State-Based Data Management
Some state partners will be managing activities for both field sampling and laboratory analyses
and would prefer to handle data management activities in-house. While NCCA encourages
states to use these in-house capabilities, it is imperative that NCCA partners understand their
particular role and responsibilities for executing these functions within the context of the national
program:
   •   If a state chooses to do
       with the following roles:
           in-house, the state will perform all of the functions associated
          o  Field Crew—including shipping/faxing of field data forms to the IM Coordinator
             (NCCA field forms must be used and the original field forms must be sent to the
             IM Center as outlined in the Field Operations Manual (EPA, 201OA))
          o  Quality Control Team for laboratory data
          o  To some extent,  Quality Assurance Manager for laboratory results
       All data will flow from the state to the NCCA IM center.  Typically, the state will provide a
       single point of contact for all things related to NCCA data.  However, it may be
       advantageous for the NCCA IM Center staff to have direct communication with the state-
       participating laboratories to facilitate the transfer of data—a point that may negotiated
       between the primary state contact, the regional coordinator and the NCCA Project
       Leader (with input from the IM Center staff).

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   •   Data transfers to NCCA IM Center must be timely. States must submit all initial
       laboratory results (i.e., those that have been verified by the laboratory and have passed
       all internal laboratory QA/QC criteria) in the appropriate format to NCCA IM Center by
       March, 2011, in order to meet NCCA product deadlines.

   •   Data transfers must be complete. For example, laboratory analysis results submitted by
       the state must be accompanied by related quality control and quality assurance data,
       qualifiers  code definitions, contaminant/parameter code cross-references/descriptions,
       test methods, instrumentation information and any other relevant laboratory-based
       assessments or documentation related to specific analytical batch runs.

   •   The state will ensure that data meet minimum quality standards and that data transfer
       files meet negotiated content and file structure standards.

The NCCA IM Center will  provide the necessary guidance for IM requirements. Each group that
will perform in-house IM functions will incorporate these guidelines as is practicable or as
previously negotiated.

4.2.    Overview of System Structure

In its entirety, the IM system includes site selection and logistics information, sample labels and
field data forms, tracking records, map and analytical data, data validation and analysis
processes, reports, and archives. NCCA IM staff provides support and guidance to all program
operations in  addition to maintaining a central data base management system for the  NCCA
data. The central repository for data and associated information collected for use by the NCCA
is a secure, access-controlled server located at WED-Corvallis. This  database is known as the
National Aquatic  Resource Surveys Information Management System (NARSIMS). The general
organization of the information management system is presented in Figure 4-1.  Data are stored
and managed on this system using the Structured Query Language (SQL). Data review (e.g.,
verification and validation) and data analysis (e.g., estimates of status and extent) are
accomplished primarily using programs developed in either (SAS) or R language software
packages.


        4.2.1.       Data Flow Conceptual  Model

The NCCA will accumulate large quantities of observational and laboratory analysis data.  To
appropriately  manage this information, it is essential to have a well-defined data flow model and
documented approach for acquiring, storing, and summarizing the data. This conceptual model
(Figure 4.2) helps focus efforts on maintaining organizational and custodial integrity, ensuring
that data available for analyses are of the highest possible quality.

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          SAMPLE SITE INFORMATION
TIER II LIST
FRAME

• Site ID
• Weighting
Factor
• Location
coordinates




LOGISTICS
DATA
• Site ID
information
• Location
coordinates
• Access
Information




SITE
VERIFICATION
DATA

• Site ID
• Measured
location
coordinates
• Sampling status
                                          INDICATOR RESEARCH AND DEVELOPMENT INFORMATION
FIELD
DATA

LABORATORY
DATA

SAMPLE
TRACKING
DATA
HISTORICAL
DATA
ASSESSMENT AND REPORTING INFORMATION
(by indicator)

ANNUAL
POPULATION
STATUS
DATA

POPULATION
TREND
DATA

SPATIAL
DATA
(CIS)


M ETA-DATA

DATA BASE
DOCUMENTATION

QUALITY ASSURANCE
DOCUMENTATION



IM SYSTEM
USER GUIDES

METHODS
DOCUMENTATION
Figure 4.1. Organization of the National Aquatic Resource Surveys Information
Management System (NARSIMS) for the NCCA.
        4.2.2.       Simplified Data Flow Description

There are several components associated with the flow of information:

   •   Communication—between the NCCA IM Center and the various data contributors
       (e.g., field crews, laboratories and the data analysis and reporting team)—is vital for
       maintaining an organized, timely, and successful flow of information and data.

   •   Data are captured or acquired from four basic sources — field data transcription,
       laboratory analysis reporting,  automated data capture, and submission of external data
       files (e.g., GIS data)—encompassing an array of data types: site characterization; biotic
       assessment; sediment and tissue contaminants; and water quality analysis. Data
       capture generally relies on the transference of electronic data, e.g., optical character
       readers and email, to a central data repository.  However, some data must be
       transcribed by hand in order to complete a record.
   •   Data repository or storage—provides the computing platform where raw data are
       archived, partially processed data are staged, and the "final" data, assimilated into a
       final, user-ready data file structure,  are stored. The raw data archive is maintained in a
       manner consistent for providing an  audit trail of all incoming records. The staging area
       provides the IM Center staff a platform for running the data through  all of its QA/QC
       paces as well has providing data analysts a first look at the incoming data. This area of
       the data system evolves as new data are gathered and user-requirements are updated.
       The final data format becomes the primary source for all statistical analysis and data
       distribution.

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       Metadata—a descriptive document that contains information compliant with the Content
       Standards for Digital Geospatial Metadata (CSDGM) developed by the Federal
       Geographic Data Committee (FGDC).


                 ECOLOGICAL INDICATOR FIELD AND LABORATORY DATA FLOW
                  FIELD DATA COLLECTION
                                             SAMPLE
                                            COLLECTION
                                                 OTHER
                                                DATA FILES
                                                (e.g., Survey
                                                design, GIS
                                                attribute data)
                                                              LABORATORY
  \ = \V RAW DATA
  SUBMISSION PACKAi
                                              INFORMATION  \
                                          MANAGEMENTCENTER\
                                             (WED-Corvallis)    \
                                                       NARS IM
                                                     SQL SERVER
                                                      Relational-
                                                   1 record per datum
Data
Table
 1
                                                   Data
                                                   Table
                                                    4
                                                        Data
                                                        Table
                                                         2
 Data
 Table

"[fata"1
 Table
                                               FINAL DATA
                                                RECORDS
                                                (Flat files)
                                                Posted to
                                               Webpage or
                                                 FTP site
FINAL DATA
 RECORDS
(EPA WATER
 QUALITY
EXCHANGE
  [WQX])
 Permanent
 Archival
     Figure 4-2. Conceptual model of data flow into and out of the master SQL database for the NCCA

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4.3.   Core Information Management Standards

The development and organization of the IM system is compliant with guidelines and
standards established by the EMAP Information Management Technical Coordination Group,
the EPA Office of Technology, Operations, and Planning (OTOP), and the ORD Office of
Science Information Management. Areas addressed by these policies and guidelines include,
but are not limited to, the following:

   •  Taxonomic nomenclature and coding;

   •  Locational data;

   •  Sampling unit identification and reference;

   •  Hardware and software; and

   •  Data catalog documentation.


The NCCA is committed to compliance with all applicable regulations and guidance concerning
hardware and software procurement, maintenance, configuration control, and QA/QC. To that
end, the NCCA team has adopted several IM standards that help maximize the ability to
exchange data within the study and with other aquatic resource surveys or similar large-scale
monitoring and assessment studies (e.g. EMAP,  R-EMAP, state probability surveys).  These
standards include those of the Federal Geographic Data Committee (FGDC 1999), the National
Spatial Data Infrastructure (NSDI 1999), and the  National Biological Information Infrastructure
(NBII 1999).  More specific information follows:

        4.3.1.       Data Formats

4.3.1.1.    Attribute Data

             •   Sql Tables

             •   Sas Data Sets.

             •   R Data Sets.

             •   Ascii Files: Comma-Separated values, or space-delimited, or fixed column

4.3.1.2.    CIS Data

             •   ARC/INFO native and export files; compressed .tar file of ARC/INFO
                workspace

             •   Spatial Data Transfer Standard (SDTS; FGDC 1999) format available on
                request

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     4.3.1.3.  Standard Coding Systems

       Sampling Site (EPA Locational Data Policy; EPA 1991)
                   Latitude and Longitude in decimal degrees ( +/- 7.4)

                   Negative longitude values (west of the prime meridian).

                   Datum used must be specified (e.g.,  NAD83, NAD27)

       Chemical Compounds: Chemical Abstracts Service (CAS 1999)

       Species Codes: Integrated Taxonomic Information System (ITIS 1999).

       Land cover/land use codes: Multi-Resolution Land Characteristics (MRLC 1999);
National Hydrography Dataset Plus Version 1.0 (NHDPIus 2005)


        4.3.2.      Public Accessibility

While any data created using public funds are subject to the Freedom of Information Act (FOIA),
some basic rules apply for general public accessibility and use.

   •   Data and metadata files are made available to the contributor or participating group for
       review or other project-related use from NARSIMS or in flat files before moving to an
       EPA approved public website.

   •   Data to be placed on a public website will undergo QA/QC review according to the
       approved Quality Assurance Project Plan.

   •   Only "final" data (those used to prepare the final project report) are readily available
       through an EPA approved public website.  Other data can be requested through the
       NCCA Project Leader or NARS Coordinator.

As new guidance and requirements are issued, the NCCA information management staff will
assess the impact upon the IM system and develop  plans for ensuring timely compliance.

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4.4.   Data Transfer Protocols

Field crews are expected to send in hard copies of field forms containing in-situ measurement
and event information to the IM Center as defined in the Field Operations Manual (EPA, 2010A).
Electronic data files are submitted by laboratories (and possibly some field crews).  Field crews
and labs must submit all sample tracking and analytical results data to the NCCA IM Center in
electronic form using a standard software package to export and format data. Examples of
software and the associated formats are:

Software                                Export Options (file extensions)

    Microsoft Excel®                      xls, xlsx, csv, formatted txt
    Microsoft Access®                    mdb, csv, formatted txt
    SAS®                                 sas7bdat, csv, formatted txt
    R                                   csv, formatted txt

All electronic files must be accompanied by appropriate documentation, e.g., metadata,
laboratory reports, QA/QC data and review results).  This information should contain sufficient
information to identify field contents, field formats, qualifier codes, etc. It is very important to
keep EPA informed of the completeness of the analyses.  Labs may send files periodically,
before all samples are analyzed, but EPA must be informed that more data are pending if a
partial file is submitted. All data files sent by the labs must be accompanied by text
documentation describing the status of the analyses,  any QA/QC problems encountered during
processing, and any other information pertaining to the quality of the data. Following is a list of
general transmittal  requirements each laboratory or state-based  IM group should consider when
packaging data for electronic transfer to the IM Center:

       •  Provide data in row/column  data file/table structure. Further considerations:
              o  Include sample id provided on the sample container label in a field for each
                 record (row) to ensure that each data file/table record can be related to a site
                visit.
              o  Use a consistent set of column labels.
              o  Use file structures consistently.
              o  Use a consistent set of data qualifiers.
              o  Use a consistent set of units.
              o  Include method detection limit (MDL) as part of each result record.
              o  Include reporting limit (RL) as part of each result record.
              o  Provide a description of each result/QC/QA qualifier.
              o  Provide results/measurements/MDL/RL in numeric form.
              o  Maintain result qualifiers, e.g., <, ND, in a separate column.
              o  Use a separate column to identify record-type. For example, if QA or QC
                data are included in  a data file, there should be a column that allows the
                 NCCA IM staff to readily identify the different result types.
              o  Include laboratory sample identifier.
              o  Include batch numbers/information so results can be paired with appropriate
                QA/QC information.
              o  Include "True Value" concentrations, if appropriate, in QA/QC records.
              o  Include a short description of preparation and  analytical methods used to
                 (where appropriate) either as part of the record or as a separate description

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                 for the test(s) performed on the sample. For example, EPAxxxx.x,
                 ASTMxxx.x, etc. Provide a broader description, e.g., citation, if a non-
                 standard method is used.
             o   Include a short description of instrumentation used to acquire the test result
                 (where appropriate). This may be reported either as part of the record  or as a
                 separate description for each test performed on the sample. For example,
                 GC/MS-ECD, ICP-MS, etc.
       •   Ensure that data ready for transfer to NCCA IM are verified and validated, and
          results are qualified to the extent possible (final verification and validation are
          conducted by EPA).
       •   Data results must complement expectations (analysis results) as specified by
          contract or agreement.
       •   Identify and qualify missing data (why is the data missing).
       •   Submit any other associated quality assurance assessments and relevant data
          related to  laboratory results (i.e., chemistry, nutrients). Examples include summaries
          of QC sample analyses (blanks, duplicates, check standards, matrix spikes) standard
          or certified reference materials, etc.), results for external performance evaluation or
          proficiency testing samples, and any internal consistency checks conducted by the
          laboratory.
Labs may send electronic files by e-mail attachments or they may upload files through a secure
FTP location.

4.5.   Data Quality and Results Validation

Data quality is integrated throughout the life-cycle of the data. Data received in to the IM center
from NCCA participants are examined for completeness, format compatibility, and internal
consistency. Field collected data quality is evaluated using a variety of automated and other
techniques. Analytical results are reviewed by subject matter experts. Any changes (deletions,
additions, corrections) are submitted to the NCCA data center for inclusion into the validated
data repository. All explanation for data changes is included in the record history.

         4.5.1.       Data Entry, Scanned, or Transferred Data

4.5.1.1.    Field crews record sampling event observational data in a standard and consistent
           manner using field data collection forms (Appendix B of the NCCA Field Operations
           Manual (EPA, 2010A).

4.5.1.2.    The IM Center either optically scans or transcribes information from field collection
           forms into an electronic format (sometimes using a combination of both processes).
           During the scanning process, incoming  data are subjected to a number of
           automated error checking routines.  Obvious errors are corrected immediately.
           Suspected errors that cannot be confirmed at the time of scanning are qualified for
           later review by someone with the appropriate background and experience (e.g., a
           chemist or aquatic ecologist). The process continues until the transcribed data are
           100 % verified or no corrections are required.

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4.5.1.3.    Additional validation is accomplished by the IM Center staff using a specific set of
           guidelines and executing a series of programs (computer code) to check for: correct
           file structure and variable naming and formats, outliers, missing data, typographical
           errors and illogical or inconsistent data based on expected relationships to other
           variables. Data that fail any check routine are identified in an "exception report" that
           is reviewed by an appropriate scientist for resolution.

4.5.1.4.    The IM Center brings any remaining questionable data to the attention of the QA
           manager and individuals responsible for collecting the data for resolution.


        4.5.2.       Analytical Results Validation

4.5.2.1.    All data are evaluated to determine completeness and validity. Additionally, the data
           are run through a rigorous inspection using SQL queries or other computer
           programs such as SAS or R to check for anomalous data values that are especially
           large or small, or are noteworthy in other ways.  Focus is on rare, extreme values
           since outliers may affect statistical quantities such as averages and standard
           deviations.

4.5.2.2.    All laboratory quality assurance (QA) information is examined to determine if the
           laboratory met the predefined data quality objectives - available through the Quality
           Assurance Project Plan (QAPP).

4.5.2.3.    All questionable data should be corrected  or qualified through the NCCA IM staff
           with support of the project QA manager.

        4.5.3.       Database Changes

4.5.3.1.    Data corrections are completed at the lowest level by the IM Center staff to ensure
           that any subsequent updates will contain only the most correct data.  Laboratory
           results found to be in error are sent back to the originator (lab) for correction by the
           IM Team. After the originator makes any corrections, the entire batch or file is
           resubmitted to the IM Center. The IM Center  uses these resubmissions to replace
           any previous versions of the same data.

4.5.3.2.    The IM Center uses a version control methodology when receiving files. Incoming
           data are not always immediately transportable into a format compatible with the
           desired file structures. When these situations occur, the IM staff creates a copy of
           the original data file which then becomes the working file in which any formatting
           changes will take place. The original raw data will remain unchanged. This practice
           further ensures the integrity of the data and provides an additional data recovery
           avenue, should the need arise.

4.5.3.3.    All significant changes are documented by the IM Center staff. The IM Center
           includes this information in the final summary  documentation for the database
           (metadata).

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4.5.3.4.    After corrections have been applied to the data, the IM Center will rerun the
           validation programs to re-inspect the data.

4.5.3.5.    The IM Center may implement database auditing features to track changes.


4.6.    Metadata

Federal Geographic Data Committee, Content standard for digital geospatial metadata, version
2.0. FGDC-STD-001-1998 (FGDC 1998).

4.7.    Information Management Operations


        4.7.1.       Computing Infrastructure

Electronic data are collected and maintained within a central server housed at the Western
Ecology Division using a Windows Server 2003 R2 (current configuration) or higher computing
platform in SQL native tables for the primary data repository and SAS® native data sets or R
datasets for data analysis. Official IM functions are conducted in a centralized environment.

        4.7.2.       Data Security and Accessibility

The IM Center ensures that all data files in the IM system are protected from corruption by
computer viruses, unauthorized access, and hardware and software failures. Guidance and
policy documents of EPA and management  policies established by the IM Technical
Coordination Group for data access  and data confidentiality are followed. Raw and verified data
files are accessible only to the NCCA collaborators.  Validated data files are accessible only to
users specifically authorized by the NCCA Project Leader. Data files in the central repository
used for access and dissemination are marked as read-only to prevent corruption by inadvertent
editing, additions, or deletions.

Data generated, processed,  and incorporated into the IM system are routinely stored as well as
archived on redundant systems by the IM team.  This ensures that if one system  is destroyed or
incapacitated, IM staff can reconstruct the databases. Procedures developed to archive the
data, monitor the process, and recover the data are described in IM documentation.

Data security and accessibility standards implemented for NCCA IM meet EPA's  standard
security authentication (i.e., username, password) process in accordance to the EPA's
Information Management Security Manual (1999; EPA Directive 2195 A1) and EPA Order
2195.1 A4 (2001D). Any data sharing requiring file transfer protocol (FTP) or internet protocol is
provided through an authenticated site.

        4.7.3.       Life Cycle

Data may be retrieved  electronically by the NCCA team,  partners and others throughout the
records retention and disposition lifecycle or as practicable (See section 4.8).

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        4.7.4.       Data Recovery and Emergency Backup Procedures

The IM Team maintains several backup copies of all data files and of the programs used for
processing the data are maintained.  Backups of the entire system are maintained off-site by the
IM Team.  The IM process used by the IM Team for NCCA uses system backup procedures.
The IM Team backs up and archives the central data base according to  procedures already
established for WED and NARSIM. All laboratories generating data and developing data files
are expected to established procedures for backing up and archiving computerized data.

        4.7.5.       Long-Term Data Accessibility and Archive

All data are transferred by OW's Water Quality Exchange (WQX) team working with the NCCA
IM Team to U.S. EPA's agency-wide WQX data management system for archival purposes.
WQX is a repository for water quality, biological, and physical data and is used by state
environmental agencies, EPA and other federal agencies, universities, private citizens, and
many others. Revised from STORET, WQX provides a centralized system for storage of
physical, chemical, and biological data  and associated  analytical tools for data analysis. Data
from the NCCA project in an Excel format will be run through an Interface Module and uploaded
to WQX by the WQX team. Once uploaded, states and tribes and the public will be able to
download data (using Oracle software) from their region.  Data will also  be provided in flat files
on the NCCA website.

4.8.    Records Management

Removable storage media (i.e., CDs, diskettes, tapes)  and paper records are maintained in a
centrally located area at the NCCA IM center by the IM Team.  Paper records will be returned to
OW once the assessment is complete.  The IM Team identifies and  maintains files using
standard divisional procedures. Records retention and disposition comply with U.S. EPA
directive 2160 Records Management Manual (July, 1984) in accordance with the Federal
Records Act of 1950.

                                 5.     INDICATORS


5.1.    Indicator S ummary


        5.1.1.       Introduction

Information common to most indicators can be found in this section.  Indicator-specific details
for each subheading in this section can be found as follows:

   •   In situ measurements - pH, dissolved oxygen, temperature, conductivity/salinity, PAR
       and secchi depth (Section 5.2);

   •   Water quality samples - total and dissolved nutrients, chlorophyll a, and phytoplankton
       (Section 5.3);

   •   Benthic macroinvertebrates (Section 5.4);

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   •   Chemistry in sediment and fish tissue - organics and inorganics (Section 5.5);

   •   Grain Size and TOC determinations (Section 5.6);

   •   Sediment Toxicity Testing (Section 5.7); and

   •   Enterococcus sample (Section 5.8).

        5.1.2.       Sampling Design

The "X-site" coordinates, predetermined by EPA, will be located using GPS and most
measurements will be collected within 0.02 nm, or ±37 m of the given coordinate.  If the crew
experiences difficulties locating an acceptable sediment grab sample, the radius, for sediment
collection, can be expanded to a maximum of 100 m for marine sites and 500 m for Great Lakes
sites. See specific procedures in the Field Operations Manual (EPA, 201OA).

        5.1.3.       Sampling and Analytical Methods

Sampling and analytical methods are specific to each indicator.  In addition to the Field
Operations Manual (EPA, 201 OA), the NCCA project team developed and provided to the field
crews a condensed description of key elements of the field activities for easy reference onsite
by field crew members. See the Sampling and Analytical Methods section for each of the
indicators described in Sections 5.2 through 5.8.

        5.1.4.       Quality Assurance Objectives

Precision objectives are presented  in tables in each of the Quality Assurance Objective sections
for each indicator.  They represent the 99 percent confidence intervals about a single
measurement and are thus based on the standard deviation of a set of repeated measurements
(n > 1).  Precision objectives at lower concentrations are equivalent to the corresponding LRL.
At higher concentrations, the  precision objective is expressed in relative terms, with the 99
percent confidence interval based on the relative standard deviation (Section 2.2.2). Objectives
for accuracy are equal to the  corresponding precision objective,  and are based on the mean
value of repeated measurements. Accuracy is generally estimated as net bias or relative net
bias (Section 2.2.2).  Precision and bias are monitored at the point of measurement (field or
analytical laboratory) by several types of QC samples described for each indicator (Quality
Assurance Objectives sections  5.2 - 5.8), where applicable, and from performance evaluation
(PE) samples.

        5.1.5.       Quality Control Procedures: Field Operations

Field data quality is addressed, in part, by application and consistent performance of valid
procedures documented in the standard operating procedures detailed in the NCCA Field
Operations Manual (EPA, 201 OA).  That quality is enhanced by the training and experience of
project staff and documentation of sampling activities.  This QAPP, the NCCA Field Operations
Manual (EPA, 201 OA), and training materials will be distributed to all field sampling  personnel.
Training sessions will be conducted by EPA and EPA Contractors to distribute and discuss
project materials.  All sampling teams will be required to view the training materials, read the
QAPP, and verify that they understand the procedures and  requirements.

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The recorded GPS measure displayed for the sampling site should be within 0.004167 decimal
degrees of latitude and longitude of the map coordinates. This distance is approximately equal
to the precision of the GPS receiver without differential correction of the position fix.

Specific quality control measures for field measurements and observations are listed in each
Quality Control Procedures section for each indicator in sections 5.2 - 5.8.

        5.1.6.      Quality Control Procedures: Laboratory Operations

An array of laboratory-based stoichiometric determinations will be conducted on a variety of
samples collected for NCCA. These analyses require extensive utilization of certified standards
for instrument calibration. Additionally, many incorporate the use of SRMs as routine QC
samples. The analytical standards and SRMs for all analyses will be provided by established,
reputable suppliers and when available, only certified materials will be used; in cases where
certified standards are not available, the analysts will obtain high purity (e.g., analytical or
reagent grade) compounds to prepare in-house standards.  Laboratory quality control
procedures are summarized in the Quality Control  Procedures section for each  indicator in
sections 5.2 - 5.8.

All laboratory instrumentation and equipment will be maintained in good repair as per
manufacturer's recommendations or best laboratory practices to ensure proper function.  If not
actual calibration, all general laboratory equipment requires some documentation of
performance. Each piece of equipment should have an assigned logbook in which the
calibration or performance records are maintained. Several pieces of equipment that may be
utilized to analyze environmental data for NCCA should have periodic maintenance and
calibration verification performed by manufacturer's representatives or service consultants.
These procedures should be documented by date  and the signature of person performing the
inspection.

Of particular interest are records for the analytical  balances used for weighing out standards or
analytical samples. These balances must be maintained under the manufacturer's
recommended calibration schedule and the performance of the balances should be verified
before each series of weighings by using a set of NIST (or previous NBS)-approved standard
weights. If the performance of a particular balance is historically stable, then the verifications
may only be  required on an appropriate periodic basis (e.g., weekly). As much as possible, the
verifications should be conducted using standard weights that reflect the magnitude of the
actual weighing. The results of the verifications should be recorded in the logbook for the
balance.
5.1.6.1.   Sample Receipt and Processing

The information management team is notified of sample receipt and any associated problems
as soon as possible after samples are received. Critical holding times for the various analyses
are the maximum allowable holding times, based on current EPA and American Public Health
Association (APHA) requirements (American Public Health Association, 2006).  Sample receipt
and processing criteria can be found in Sample Receipt and Processing sections for each
indicator in Sections 5.2-5.8.  Sample residuals are retained by each laboratory until the  EPA
Project Lead has authorized the disposition of samples.

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5.1.6.2.    Analysis of Samples

Each of the laboratory analyses will be conducted in accord with generally accepted laboratory
procedures such as those described in Standard Methods for the Examination of Water and
Wastewater or U.S. EPA Methods. Appropriate QC samples (e.g., standards, reagent blanks,
duplicates, and standard reference materials) will be run with each batch of samples. If the
prescribed quality criteria are not consistently met, the analyst will confer with the laboratory
supervisor for corrective measures before proceeding with additional samples. Analytical
quality control criteria can be found in the Analysis of Samples section for each indicator in
Sections 5.2 - 5.8.

5.1.6.3.    Data Reporting, Review, and Management

The data analysis teams and the project leads are ultimately responsible for ensuring the
validity of the data,  although performance of the specific checks may be delegated to other staff
members.   Once data have passed all acceptance requirements, computerized data files are
prepared in a format specified for the NCCA project.  The electronic data files are transferred to
the NCCA IM Coordinator at WED-Corvallis for entry into a centralized data base.  A hard copy
output of all files will also be sent to the NCCA IM Coordinator. See section 4.2 for data
management procedures, once it reaches the IM Coordinator.

5.2.    In Situ Measurements

The first activities that should be conducted upon arriving onsite are those that involve water
column measurements;  these data need to be collected before disturbing bottom sediments.


        5.2.1.       Introduction

In situ measurements made using field meters are recorded on standardized data forms.  Field
crews will measure dissolved oxygen (DO), pH, conductivity  (fresh water) or salinity (marine),
and temperature using a multi-parameter water quality meter. A  meter will be used to read
photosynthetically active radiation (PAR) throughout the photic zone.  Secchi disk depth will also
be measured.  At Great Lakes sites, underwater video will be taken at each site.

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Table 5.2-1. NCCA In situ Indicators.
Measure/Indicator
Water
Quality
Dissolved
oxygen
Salinity
(marine),
temperature,
Depth,
Conductivity
(freshwater)
Secchi/light
measurements
PAR
PH
Specific data type
Observable on-site
Observable on-site
Observable on-site
Observable on-site
Assessment
outcome
Hypoxia/anoxia
Water column
characterization
Societal value
and ecosystem
production
Water column
characterization
        5.2.2.
Sampling Design
At the index site - the site established for sampling within 37m of the X point, the secchi depth
is recorded and a vertical profile of in situ or field measurements (temperature, pH, DO,
conductivity or salinity and PAR) at various depths is conducted to provide a representation of
the coastal area's condition throughout the water column.

Parameter readings for the indicators in Table 5.2.1  will be taken  as follows:

0.1 m -_ 0.5 m (near-surface) and every 1-m interval to 10 m, then at 5-m intervals, thereafter, to
near-bottom (0.5 m off-bottom).

The underwater video camera is lowered until a clear image of the bottom can  be  seen on the
screen.

        5.2.3.       Sampling and Analytical Methods

Multiparameter Readings:

Because of the multiple field crews to be involved in NCCA 2010, an array of water quality
instrumentation will be employed for water column profiling. Basic water quality parameters will
be measured by using  either a self-contained SeaBird CTD, or similar unit, to electronically log a
continuous profile of the water column or by using hand-held multiparameter water quality
probes (e.g., Hydrolab Surveyor or YSI Sondes) with cable connection to a  deck display. In
cases where CTD units record data electronically, the measurements  must  be  transferred to the
field data sheet before leaving the index site.

Prior to conducting a CTD cast, the instrument will be allowed 2-3 minutes of warmup while
being maintained at near the surface, after which, the instrument will be will slowly lowered at
the rate of approximately 1  meter per second while performing the down cast.

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Near-bottom conditions will be measured at 0.5 m off bottom with both instrument types by first
ascertaining on-bottom (e.g., slake line/cable), then pulling up approximately 0.5 m. The crews
must then allow 2-3 minutes for disturbed conditions to settle before taking the near-bottom
measurements. The profile will be repeated on the ascent and recorded for validation purposes,
but only data from the down trip will be the  reported in the final data.

PAR Readings:

Measurements of light penetration, taken by hand-held light meters, will be recorded for
conditions at discrete depth intervals in a manner similar to that for profiling water quality
parameters with the hand-held probe. The  underwater (UW) sensor will be hand lowered at the
regime described and at each discrete interval, and at each depth inmterval the deck reading
and UW reading will be recorded. If the light measurements become negative before reaching
bottom, the measurement terminates at that depth. The profile will be  repeated on the ascent.

Secchi Depth Readings:

Secchi depth will be determined by using a standard 20-cm diameter black and white secchi
disc. The disc will be lower to the depth at which it can no longer be discerned, then it is slowly
retrieved until it just reappears; that depth is marked and recorded as  secchi  depth (rounded to
the nearest 0.5 m). This process is repeated two additional times  for a total of three depth
readings for each disappear/reappear measurement.

Unerwater Video (Great Lakes sites only):

Detailed instructions on operation of the underwater video equipment  can be found  in the Field
Operations Manual (EPA, 201OA).  A component diagram is included.


        5.2.4.       Quality Assurance  Objectives

Several pieces of equipment that may be utilized to collect or analyze environmental data for
NCCA should have periodic maintenance and calibration verification performed by
manufacturer's representatives or service consultants. These procedures should  be
documented by date and the signature of person performing the inspection. Examples include:

CTDs - annual maintenance and calibration check by manufacturer or certified service center;

Light (PAR) Meters - biannual verification of calibration coefficient by manufacturer;

   •   Multiparameter probes - as needed maintenance and calibration check by manufacturer
       or certified service center.
   •   Video cameras- as needed maintenance as described in the manufacturer information.

All other sampling gear and laboratory instrumentation will be maintained in good repair as per
manufacturer's recommendations or common sense to ensure proper function.

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Measurement data quality objectives (measurement DQOs or MQOs) are given in Table 5.2-2.
General requirements for comparability and representativeness are addressed in Section 2. The
MQOs given in Table 5.2-2 represent the maximum allowable criteria for statistical control
purposes.


Table 5.2-2.  Measurement data quality objectives: water indicators.
Variable or
Measurement
Oxygen, dissolved
Temperature
Conductivity
Salinity
Depth
PH
PAR
Secchi Depth
Maximum
allowable Accuracy
Goal (Bias)
±0.5 mg/L
±1 ±C
±1 uS/cm
±1 ppt
±0.5 m
±0.3 SU
0.01 umol s"1 m"2*
±0.5 m
Maximum
Allowable
Precision
Goal (%RSD)
10%
10%
10%
10%
10%
10%
5%
10%
Completeness
95%
95%
95%
95%
95%
95%
95%
95%
       "Determined by biannual manufacturer calibration.
        5.2.5.
Quality Control Procedures: Field Operations
For in situ measurements, each field instrument (e.g., multi-probe) must be calibrated, inspected
prior to use, and operated according to manufacturer specifications. Figure 5.2.1 illustrates the
general scheme for field chemistry measurement procedures.  If problems with any field
instrument are encountered, the user should consult the manufacturer's manual, and/or call the
manufacturer prior to sampling. To ensure that field measurements meet the accuracy goals
established for NCCA, quality controls checks are performed on a regular basis (daily during
sample collection) for most of the field equipment/instruments used to generate monitoring data.
When QC checks indicate instrument performance outside of NCCA acceptance criteria, the
instrument will be calibrated (for those instruments that allow adjustments) against an
appropriate standard to re-establish acceptable level of performance; the procedure will be
documented on field data forms.

Some instruments have fixed functions that cannot be  adjusted under field condition. In cases
where these types of measurements fail the field-QC checks, the degree of variance will be
documented in field records; if possible, the situation will be rectified by changing out the faulty
equipment with a backup unit until the failed unit can be repaired.  If no backup is available,
depending on the relative importance of that particular measurement to overall success of the
monitoring operation, the crew chief must decide whether to continue operations with slightly
compromised or deficient data or to suspend sampling until the situation is corrected. For
example, if the GPS system was found to be totally unreliable, sampling activities should be
suspended until a reliable unit was in place; to continue field operations without GPS to locate
sampling sites would have dire consequences to the study design. On the other hand, if a pH
probe were to break or become faulty, sampling could  continue without seriously compromising

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the overall characterization of the environmental condition for a site. It becomes a judgement
call, and if the crew has difficulty in making a decision, they should call their State QA
Coordinator for guidance.

Proper maintenance and routine calibration checks are the key elements related to quality
control for these instruments. Calibration of the CTD units is an involved procedure that is
usually performed only periodically (e.g., semiannually) and at a center that is equipped for that
function; however, the instruments have an established track record and tend to be reliable for
the intervals between calibrations. The calibration procedures will follow those prescribed by
Sea-Bird Electronics and should be performed at a facility set up for that purpose. Monthly
calibration checks will  be performed in the laboratory.  In-field calibration checks will be
conducted on a daily basis when the CTD unit is in use to document the instrument's
performance. The multiparameter probe/deck display units, on-the-other-hand, are easy to
calibrate; these units will undergo QC checks on a daily basis and be calibrated if out of
tolerance.  Calibration requirements and QC checks for the various instruments are described in
the following sections.

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                   FIELD MEASUREMENT PROCESS: WATER CHEMISTRY INDICATOR
                                        PRE-DEPARTURE CHECK
                                         Probe Inspectnon
                                         Electronic Checks
                                         Test Calibration
                                                     and/or Instrument
                                         F ELD CAL BRAT ON
                                        QC Sample Measurement
                                        Performance Evaluation
                                        Measurement
                                             CONDUCT
                                          MEASUREMENTS
                                         AND RECORD DATA
                                        QC Sample Measurement
                                        Duplicate Measurement
                                             REVIEW
                                            DATA FORM
 Qualify Data
Correct Errors
                                       ACCEPT FOR DATA ENTRY
Figure 5.2.1. Field Chemistry Measurement Procedures.

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Seabird CTDs:

SeaBird CTDs are routinely used in deep water or oceanographic surveys to measure and
electronically log various water column parameters. When properly maintained and serviced,
they have an established history of dependable utilization. The units can be configured with
different arrays of probes; for the purposes of the NCCA, the units should be equipped to
measure DO, temperature, salinity/conductivity, pH, and depth.

Because in-the-field calibrations of CTDs are not feasible, QC checks on the core parameters
will be conducted daily either by taking water samples from known depths and analyzing them
later for DO (field fixed for Winkler titration), pH, and salinity and comparing those results with
the logged water column data at the depth, or by conducting a side-by-side, realtime
comparison against another water quality monitoring probe (e.g., multiparameter probe). Depth
measurement on bottom can  be confirmed onsite by comparing the CTD reading to that on the
vessel's depth finder display (not meant to  imply that the vessel's depth finder is more accurate,
just a quick confirmation that  the two instruments are in the same ballpark). The QC check
information will be recorded on standardized data forms. The CTD's serial number or property
ID will be used to identify the  unit; the person performing the QC checks will initial and date the
data form.

A failed QC check for the CTD should initiate an immediate check of the instrument for obvious
signs of malfunction (e.g., loose connections or plugged lines). If the instrument cannot be
brought into acceptable tolerances, the data files must be flagged as being out of compliance
and a description of the problem will be noted on the field data form.  See criteria in Table 5.2-3.
Table 5.2-3. Field quality control: CTD indicator.
Check Description
DO check - compare to
Winkler or DO meter
Salinity check - compare
to pH meter
pH check - compare to pH
meter
Conductivity - check
against calibration
standard
Frequency
Daily
Daily
Daily
Daily
Acceptance Criteria
±1.0mg/L
± 0.2 ppt
> 5.75 and < 8.: ±0.15
< 575 or > 8.25: ± 0.08
±2 uS/cm or ±10%
Corrective
Actions
Check for loose wires etc. Flag
data.
Check for loose wires etc. Flag
data.
Check for loose wires etc. Flag
data.
Check for loose wires etc. Flag
data.

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Multiprobe Profiling Instrument:
Multiprobe instruments require calibration checks on a daily basis during periods of use. The
instrument is used to make instantaneous (real time) measurements that are read from a
deckside display unit while the probe is lowered and raised at discrete depth intervals (e.g., at 1-
m increments) through the water column. Calibration procedures are described in  detail in the
Operating Manuals (and Performance Manual) of the specific instrument. The units will be used
in applications to measure DO, salinity, pH, temperature, and depth. Discussion of the
calibration procedures and standards specific to the individual parameters  follows.

DO will be calibrated by allowing the probe to equilibrate in an air-saturated-with-water
environment, which represents 100% DO saturation at conditions of standard atmospheric
pressure (760  mm Hg). This environment is established by positioning the  polarographic DO
sensor in a calibration cup that is filled with freshwater to a level just below the surface of the
sensor's membrane and then  placing a lid or cover over the cup to create a saturated humidity.
When equilibrium is attained, the operator will activate the instrument to accept the condition as
the calibration  input for 100%  DO saturation. Once calibrated, a properly functioning instrument
should hold its DO calibration  from day to day with  only a slight drift of 2-3% from the 100%
saturation standard; drift exceeding that level is indicative of the need to change the membrane
and electrolyte solution.

The pH probe  requires the establishment of a two point calibration curve using two standard
buffer solutions to bracket the nominal range of pH expected to be measured. For NCCA 2010,
standard buffers of pH 7.0 and 10.0 will be used to calibrate the equipment. The buffer solutions
must be commercially supplied with accuracy of ± 0.02 pH units (or better), referenced to NIST
SRMs; calibration solutions should be replaced with fresh buffer every 3-4  days.

The conductivity/salinity cell will  be calibrated using a primary conductivity/seawater standard.
A secondary, seawater standard that has had its salinity referenced against a certified standard
may be used. These procedures and results data for the preparation of the secondary standard
will be logged  into a QA notebook that will be maintained by the State  Field Coordinators or  in-
house QA personnel. Salinity of the seawater standard should be generally representative of the
conditions expected in the field (e.g., for NCCA 2010, a mid-range salinity, 20-30 ppt). A bulk
supply (5 gal) of the secondary standard can be maintained in a central location and field crews
should replace their calibration allotments (300- 500 ml portions) with fresh standard every 3-4
days, or at any time that it becomes suspect.

The depth sensor (a pressure transducer) is calibrated to 0.0 m of depth while the instrument is
non-immersed (absence of water pressure); this in  effect becomes the standard for depth
calibration.

The temperature function of the  instruments are set by the manufacturer and can not be
adjusted or calibrated in the field. As part of the daily calibration checks, the instrument's
temperature reading will  be compared to that of a hand-held laboratory thermometer (accuracy,
±1°C) as a pass/fail screen.
For each of the water quality parameters, the program has established a maximum range of
allowable difference that the instrument may deviate from calibration standard (Table 5.2-4). It
should be noted that while these limits are acceptable for the purpose of qualifying field

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     measurements taken with the unit, when performing the daily QC check, crews should set the
     instrument to as near the standard as possible. The daily QC checks should not require more
     than slight adjustments to bring the instrument into agreement. If an instrument's performance
     becomes erratic or requires significant adjustments to calibrate, the unit should be thoroughly
     trouble-shot; problems generally can be determined as being probe-specific or related to power
     source (e.g., low battery voltage or faulty connections). Routine maintenance and cleaning
     should be performed as per the manufacturer's recommendation.

     Failed calibration checks should initiate a thorough inspection of the unit for obvious sign of
     malfunction (e.g., loose connections, damaged probes, power source, fouling on DO
     membrane, etc.). After any maintenance required to correct problems, the unit will be re-
     calibrated with documentation on the appropriate field data form. In most cases, unless a probe
     is actually broken or damaged, the instrument can be corrected in the field. If the unit will
     calibrate within the guidelines, continue with the water column measurements. If one or more
     parameters remain suspect, fully document the nature of the problem on the field. Depending on
     the importance of the suspect parameter, the site may require a revisit to log an acceptable
     water column profile. Of course, it is always advisable to have a backup instrument available.
     Table 5.2-4.  Field quality control: multiparameter meter indicator.
  Check Description
    Frequency
 Acceptance Criteria
           Corrective
            Actions
Verify performance of
temperature probe using
wet ice.
Prior to initial
sampling, daily
thereafter
Functionality = ± 0.5°C
See manufacturer's directions.
Verify depth against
markings on cable
Daily
±0.2 m
Re-calibrate
pH  - check against
calibration standards
At the beginning
and  end of each
day
>5.75 and< 8.: ±0.15
< 575 or > 8.25: ± 0.08
AM: Re-calibrate
PM: Flag day's data. pH probe
may need maintenance.
Conductivity - check
against calibration
standard
At the beginning
and  end of each
day
±2 uS/cm or ±10%
AM: Re-calibrate
PM: Flag day's data.  Instrument
may need repair.
Salinity - check against
calibration standard
At the beginning
and  end of each
day
± 0.2 ppt
AM: Re-calibrate
PM: Flag day's data. Instrument
may need reapair.
Check DO calibration in
field against
atmospheric standard
(ambient air saturated
with water)
At the beginning
and  end of each
day
±1.0 mg/L
AM: Re-calibrate
PM: Flag day's data. Change
membrane and re-check.

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LI COR PAR meter:
No daily field calibration procedures are required for the LICOR light meter; however, the
manufacturer recommends that the instrument be returned to the factory for bi-annual
calibration check and resetting of the calibration coefficient. Calibration kits are available from
LICOR and this procedure can be performed at the laboratory (see LICOR operation manual).
There are several field QC measures to help ensure taking accurate measurements of light
penetration. The "deck" sensor must be situated in full sunlight (i.e., out of any shadows).
Likewise, the submerged sensor must be deployed from the sunny side of the vessel and care
should be taken to avoid positioning the sensor in the shadow of the vessel. For the
comparative light readings of deck and submerged sensors, (ratio of ambient vs. submerged),
the time interval between readings should be minimized (approximately 1 sec).

Secchi Disk:

No field calibration procedures are required for the Secchi disk. QC procedures, when using the
Secchi disk to make water clarity measurements, include designating a specific crew member
as the Secchi depth reader; take all measurements from the shady side of the boat (unlike
LICOR measurements which are taken from the sunny side); and do not wear sunglasses when
taking Secchi readings.

Underwater Video (Great Lakes only):

No field calibration of camera is required but it should be checked prior to each field day to
assure that it is operational.  The battery should be charged regularly.


        5.2.6.       Quality Control Procedures: Laboratory Operations

There are no laboratory operations associated with this indicator.

        5.2.7.       Data Reporting, Review, and Management

Data reporting  units and significant figures are given in Table 5.2-5.

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Table 5.2-5. Data reporting criteria: field measurements.
Measurement
Dissolved Oxygen
Temperature
PH
Conductivity
Salinity
PAR
Depth
Secchi Depth
Units
mg/L
°C
pH units
u.S/cm at 25 °C
ppt
mE/m^/s
meters
meters
No.
Significant
Figures
2
2
3
3
2
2
2
2
Maximum No.
Decimal Places
1
1
1
1
1
1
0.5
0.5
5.3.   Water Quality Measurements
        5.3.1.
Introduction
Conditions of water quality will be evaluated for each NCCA station through the analyses of
indicators of anthropogenic enrichment, including nutrient levels, chlorophyll a content and
phytoplankton. See Table 5.3-1 for indicators and data types.
Indicators based on algal community information attempt to evaluate coastal condition with
respect to stressors such as nutrient loading.  Data are collected for chlorophyll a to provide
information on the algal loading and gross biomass of blue-greens and other algae within each
lake. Phytoplankton are free-floating algae suspended in the water column, which provide the
base of most food webs. Excessive nutrient and organic inputs from human activities lead to
eutrophication, characterized in part by increases in phytoplankton biomass. Both species
composition and abundance respond to water quality changes caused by nutrients, pH,
alkalinity, temperature, and metals.
Table 5.3-1  National Coastal Condition Assessment Indicators.
Measure/Indicator
Water Quality

Phytoplankton
Nutrients
Chlorophyll
Great Lakes only
Specific data type
Filtered surface sample for
dissolved inorganic NO2 NO3, NH4,
PO4; Unfiltered surface sample for
Total N and P
chlorophyll a
Phytoplankton
Assessment
outcome
Nutrient
enrichment
Algal community

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The Field Operations Manual (EPA, 201OA) contains a step by step process used to archive
video footage. Video file names use the following format:  DVRyymmdd_hhmm_xxx.avi.
        5.3.2.       Sampling Design

Water chemistry and phytoplankton (Great Lakes only) samples are collected at the index site.
At a discrete depth of 0.5 m.

        5.3.3.       Sampling and Analytical Methods

Collection:

Sample collection using a Van Dorn sampler, Niskin bottle or peristaltic pump will be followed by
field processing of chlorophyll a and soluble nutrient samples. From the sampler, two bottles
will be filled; a 250 ml_ brown Nalgene bottle for total nutrients and a 2-liter wide-mouth brown
Nalgene container for chlorophyll and soluble nutrients.  At Great Lakes sites a 1 L brown
Nalgene bottle will be filled and 2 mL of Lugol's solution will be added within 2 hours of sample
collection for phytoplankton.

Filtration:

Chlorophyll and dissolved nutrients samples will be obtained by filtering site water (collected at
the depth regimes described in Section 5.3.2) and retaining the filter with filtered material for the
analyses of chlorophyll  a; the filtrate will be used for the analyses of soluble nutrients.
Chlorophyll samples will be collected by filtering up to  2 L of site water (or sufficient volume to
produce a visible green residue on the filter) through the 47 mm  GFF; the volume of sample
water filtered must be recorded on the field data form and on the label  on the centrifuge tube in
which the filter is stored. After filtration, the filter is kept frozen in a tin-foil covered centrifuge
tube.  It is shipped to the laboratory on wet ice.  The dissolved nutrient sample will be collected
by pouring approximately 200 ml of the filtrate into a clean 250 ml Nalgene bottle. The sample
will be capped and placed on ice until it is shipped to the laboratory. Detailed procedures for
sample  collection and processing are described in the Field Operations Manual (EPA, 201 OA).
Laboratory:
The basic laboratory methods for these analyses will be:

   •   chlorophyll a analysis - acetone extraction, fluorometric analysis
total and soluble nutrients - spectrophotometry (autoanalyzer)

Phytoplankton identification and enumeration

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Nutrient Chemistry:

The analytical method for both saltwater and freshwater ammonia samples is based upon the
indophenol reaction adapted to automated gas-segmented continuous flow analysis. Freshwater
ammonia samples are buffered at a pH of 9.5 with a borate buffer in order to decrease
hydrolysis of cyanates and organic nitrogen compounds, and are distilled into a solution of boric
acid.

To obtain a nitrate concentration, a sample is passed through a column containing granulated
copper/cadmium to reduce nitrate to nitrite. The nitrite (that was originally present plus reduced
nitrate) is determined by diazotizing with sulfanilamide and coupling with N-(l-naphthyl)-
ethylenediamine dihydrochloride to form a  highly colored azo dye which is measured
colorimetrically.

The recommended method for total nitrogen is  persulfate digestion followed by analysis by
cadmium reduction. The cadmium column reduces nitrate to nitrite which is determined by
diazotization with sulfanilamide.

As an alternative, total nitrogen can be calculated by adding the total kjeldahl nitrogen (TKN)
result to the nitrate+nitrite-as-nitrogen result. The TKN procedure converts nitrogen components
of biological origin such as amino acids, proteins and peptides to ammonia. The sample is
heated in the presence of sulfuric acid, H2SO4,  cooled, diluted and analyzed for ammonia.

For both undigested orthophosphate samples and digested total phosphorus samples,
ammonium molybdate and antimony potassium tartrate react in an acid medium with dilute
solutions of phosphorus to form an antimony-phosphomolybdate complex.  This complex is
reduced to an intensely blue-colored complex by ascorbic acid. The color is proportional to the
phosphorus concentration. Total phosphorus in both freshwater and saltwater requires a
manual persulfate digestion to convert organic  phosphorus compounds to orthophosphate.

Chlorophyll:

Chlorophyll a content of phytoplankton filtered from a known volume of site-collected water will
be analyzed fluorometrically in the laboratory. The recommended method is a non-acidification
variation of EPA  Method 445.0: "In Vitro Determination of Chlorophyll a and Pheophytin a in
Marine and Freshwater Phytoplankton by Fluorescence" (Arar and Collins,  1992). Pigments are
extracted from the filter with 90 % acetone, with the aid of a mechanical tissue grinder.
Fluorescence of the extract is measured to determine chlorophyll a concentration.

Phytoplankton:

The modified utermohl method will be used for  phytoplankton samples. This involves a
microscopic examination of a preserved watr sample for soft bodied algae and a second
examination is performed on a cleaned diatom  preparation for identification and enumeration.

        5.3.4.       Quality Assurance  Objectives

MQOs are given in Table 5.3-2 and 5.3-3.  General requirements for comparability and
representativeness are addressed in Section 2. The MQOs given in Table 5.3-2 and 5.3-3
represent the maximum allowable criteria for statistical control purposes. LT-MDLs are

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monitored over time by repeated measurements of low level standards and calculated using
Equation 1a.
Table 5.3-2.   Measurement data quality objectives: water chemistry indicator.
Variable or
Measurement
Ammonia
Nitrate
Phosphorus,
total and ortho
Nitrogen, total
Nitrate- Nitrite
(NO3-NO2)
Chlorophyll a
Method
Detection
Limit
0.01 mg/l
NH3-N marine
(0.7 ueq/L)
0.02 mg/l NH3-
N freshwater
0.01 mg/l
NO3-N marine
(10.1 ueq/L)
0.03 mg/l NO3-
N freshwater
0.002 mg/L
0.03 mg/L
0.01 mg/l
NOX-N marine
0.02 mg/l NOX-
N freshwater
1.5ug/L
Precision
Objective
±0.01 mg/L or ±10%
±0.01 mg/L or ±5%
±0.002 mg/L or
±10%
±0.01 mg/L or ±10%
±0.01 mg/l or ±10%
± 1.5 ug/Lor±10%
Accuracy
Objective
±0.01 mg/L
NH3-N or
±10%
±0.01 mg/L
NO3-N or
±5%
±0.002
mg/L P or
±10%
±0.01 mg/L
Nor ±10%
± 0.01 mg/l
NOx-N or
±10%
± 1.5ug/L
or ±10%
Transition
Value3
0.10 mg/L
0.1 mg/L
0.02 mg/L
0.1 mg/L
0.10 mg/L
15 ug/L
Completeness
95%
95%
95%
95%
95%
95%
NA = not applicable
a
 Represents the value above which precision and bias are expressed in relative terms.

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Table 5.3-3.  Measurement data quality objectives: phytoplankton indicator.
      Variable or
     Measurement
   QA Class
Expected Range
  and/or Units
        Summary of Method
 Concentrate
 Subsamples
       N
      NA
Concentrated by settling and decanting
or by centrifugation to 5-10 times the
original whole-water sample
 Counting cell/
 Chamber preparation
       N
      NA
Prepare either Palmer-Maloney
counting cell or Utermohl sedimentation
chamber
 Enumeration
                0 to 30 organisms
                  Random systematic selection of field or
                  transect with target of 300 organisms
                  from sample
 Identification
                     genus
                  Specified keys and references
        5.3.5.
Quality Control Procedures: Field Operations
Throughout the water chemistry sample collection process it is important to take precautions to
avoid contaminating the sample. Samples can be contaminated quite easily by perspiration
from hands, sneezing, smoking, suntan lotion, insect repellent, fumes from gasoline engines or
chemicals used during sample collection.

The sampler will be cleaned with Alconox, and rinsed well with tap water or Dl, and at the next
site, it will be rinsed three timeswith site water. A small amount (-500 ml) of the collected water
should be used to rinse the reservoir before adding the remainder of the water for sample
processing. All field collection and processing implements will be maintained in a clean
environment.  Care must be taken in general to set up  in  a relatively clean work space for the
filtering process.

Chlorophyll can degrade rapidly when exposed to bright light.  It is important to keep the sample
on ice and in a dark place (cooler) until it can be filtered.  If possible, prepare the sample in
subdued light (or shade) by filtering as quickly as possible to minimize degradation.  If the
sample filter clogs and the entire sample in the filter chamber cannot be filtered, discard the filter
and prepare a new sample, using a smaller volume.

Phytoplankton samples collected at Great Lakes sites must be preserved with  Lugol's solution
within 2 hours of sample collection and the presence of preservative should be noted on the
Sample Collection Form. Samples should be stored on ice or refrigerated.
See Tables 5.3-4 through 5.3-6 for quality control activities and corrective actions.

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Table 5.3-4.  Sample processing quality control activities: water chemistry
indicator.
Quality Control
Activity
Total Nutrients
Containers and
Preparation
Sample Storage
Holding time
Filtration
Description and Requirements
Rinse collection bottles 2 times with ambient
water to be sampled
Store samples in darkness at 4°C
Monitor temperature daily
Complete filtration of dissolved nutrient
samples (and chlorophyll) within 48 hours of
collection.
0.7 |o,m GFF filters required for all dissolved
analytes. Rinse the filter flask with 10-20 ml_
of filtrate and discard. Rinse aliquot bottles
with two 25 to 50 ml_ portions of filtered
sample before use.
Corrective Action

Qualify sample as suspect
for all analyses
Qualify samples
Re-collect filtrate.

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Table 5.3-5. Sample processing quality control: chlorophyll a indicator.
Quality Control
Activity
Holding time
Filtration (done
in field)
Sample Storage
Description and Requirements
Complete filtration of chlorophyll within 48
hours of collection.
Whatman 0.7 |o,m GF/F (or equivalent) glass
fiber filter. Filtration pressure should not
exceed 15 psi to avoid rupture of fragile algal
cells.
Store samples in darkness and frozen (-20 °C)
Monitor temperature daily
Corrective Action
Qualify samples
Discard and refilter
Qualify sample as suspect
Table 5.3-6. Sample processing quality control: phytoplankton indicator.
Quality
Control
Activity
Preservation
Sample
Storage
Description and Requirements
Preserve with Lugols within 2 hours of collection.
Store samples on wet ice
Corrective Action
Re-collect
Qualify sample as suspect
        5.3.6.
Quality Control Procedures: Laboratory Operations
Although the following is not a complete list, it will serve to indicate the degree of quality
expected for analytical standards used to calibrate and verify analytical instrumentation:
Analyses of indicators in water:

Chlorophyll - Chi a extract from Anacystis (Sigma Chemicals)
Nutrients - certified standards from a reputable supplier

Instrumentation that may require periodic maintenance and calibration verification:
Analytical Balances - annual verification by service representative;
Analytical Instrumentation (AutoAnalyzer, etc.) - as per need based on general performance;
service contracts recommended.
All other sampling gear and laboratory instrumentation will be maintained in good repair as per
manufacturer's recommendations or common sense to ensure proper function.

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     5.3.6.1. Sample Receipt and Processing

QC activities associated with sample receipt and processing are presented in Table 5.3-7.
Several additional aliquots are prepared from the bulk water samples. Ideally, all analyses are
completed within a few days after processing to allow for review of the results and possible
reanalysis of suspect samples within seven days. Analyses of samples after the critical holding
time (Table 5.3-7) is exceeded will likely not provide representative data.
Table 5.3-7.
indicator.
Sample receipt and processing quality control: water chemistry
Quality Control
Activity
Sample Log-in
Sample Storage
Holding time
Description and Requirements
Upon receipt of a sample shipment, laboratory
personnel check the condition and
identification of each sample against the
sample tracking record.
Freeze samples upon receipt, until analysis
Holding times for nutrient samples are
extended when samples are stored frozen.
Chlorophyll holding time is 28 days to extract
and 21 days to analyze.
Corrective Action
Discrepancies, damaged, or
missing samples are reported
to the IM staff, QAPP project
manager, and indicator lead
(if identified)
Qualify sample as suspect for
all analyses
Qualify samples
     5.3.6.2. Analysis of Samples

QC protocols are an integral part of all analytical procedures to ensure that the results are
reliable and the analytical stage of the measurement system is maintained in a state of
statistical control.  Figure 5.3-1 illustrates the general scheme for analysis of a batch of water
chemistry samples, including associated QC samples.

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     PREPARE QC SAMPLES
   Laboratory Blank
   Fortified Sample
   Laboratory Split Sample
                               PREPARE QC SAMPLES
SAMPLEPROCESS NG
                                                                      QC Check Samples (QCCS)
                                                                      Internal Reference Sample

                                                                Contamination
                                                                  or Biased
                                                                 Calibration
    Laboratory
      Blank
                                                                Recheck
                                                              LT-MDL QCCS
                        Insert randomly
                       into sample batch
                                          Calibration
                                            QCCS
           Accept Batch
             for Entry
           and Verification
                                                                  (Re-Calibrate
                                                                   Re-analyze
                                                                 Previous Samples
    Calibration
      QCCS

                                  Pass  ^Calibration^  Fail
         f  Qualify batch
            for possible
         L  re-analysis
Figure 5.3-1. Laboratory Sample Processing.

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Nutrient Analyses and Water Chemistry:

Information regarding QC sample requirements and corrective actions, for nutrient and water
chemistry samples, are summarized in Table 5.3-8. Total and dissolved nutrients (i.e., nitrates,
nitrites, phosphates, total nitrogen and ammonia) will be measured by using automated
spectrophotometry. Analytical sets or batches should be held to 25 or less and must include
appropriate QC samples uniquely indexed to the sample batch. The minimum QC samples
required for nutrient analysis on a per batch basis include  a four point standard curve for each
nutrient of interest;  reagent blanks at the start and completion of a run; one duplicated sample;
and one reference treatment for each nutrient.  The performance criteria for an acceptable batch
are: accuracy - the  reported measurements for the reference samples be within 90-110% of the
true value for each  component nutrient and, precision - a relative percent difference between
duplicate analyses of <30% for each component nutrient. Any batch not meeting the QA/QC
requirements will be re-analyzed.

If certified reference solutions are not readily available, the laboratory may prepare its own
laboratory control treatments (LCT) by spiking  filtered seawater with the nutrients of interest.
The concentration of the each component should be sufficient to result in a good instrument
response while at the same time, remain environmentally realistic. For the LCT to be
acceptable, the laboratory must demonstrate nominal recovery efficiencies of 95% for each
component.
Table 5.3-8. Laboratory quality control samples: water chemistry indicator.
QC Sample Type
(Analytes), and
Description
Laboratory/
Reagent Blank
Quality Control
Check Sample
(QCCS):
Prepared so
concentration is
four to six times
the LT-MDL
objective.
Calibration QCCS:
Frequency
Once per day
prior to
sample
analysis
Once per day
Before and
after sample
analyses
Acceptance
Criteria
Control limits

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Laboratory
Duplicate Sample:
(All analyses)
One per
batch
<30%
If results are below LRL:
Prepare and analyze split from different sample
(volume permitting). Review precision of QCCS
measurements for batch. Check preparation of
split sample. Qualify all samples in batch for
possible reanalysis.
Matrix spike
samples: (Only
prepared when
samples with
potential for matrix
interferences are
encountered)
One per
batch
Control limits
for recovery
cannot exceed
100±20%
Select two additional samples and prepare
fortified subsamples.  Reanalyze all suspected
samples in batch by the method of standard
additions.  Prepare three subsamples
(unfortified, fortified with solution approximately
equal to the endogenous concentration, and
fortified with solution approximately twice the
endogenous concentration.
 Chlorophyll a Analysis:

 The QA/QC requirements for chlorophyll analysis require that the laboratory first successfully
 complete an initial demonstration of capability prior to conducting analyses of the field samples.
 This exercise includes the determination of a linear dynamic range (LDR) using a series of
 chlorophyll  stock standard solutions prepared from commercially available standards as
 described in Standard Method 445.0. Also, the laboratory should determine and report both
 instrument detection limits (IDLs) and MDLs. Upon the establishment of an LDR, the
 performance of the instrument should be verified by the analysis of an SRM (e.g., Sigma -
 Anacystis).

 During the routine analyses of chlorophyll  samples, a batch should consist of up to 25 field
 samples. The  performance criteria for an  acceptable batch are shown in Table 5.3-9.
 Table 5.3-9. Laboratory quality control samples: chlorophyll a indicator.
QC Sample
Type
(Analytes),
and
Description
Laboratory/
Reagent
Blank
Calibration
QCCS:
Frequency
Once per day
prior to
sample
analysis
Before and
after sample
analyses
Acceptance
Criteria
Control limits <
LRL
±10% or method
criteria
Corrective Action
Prepare and analyze new blank. Determine and
correct problem (e.g., reagent contamination,
instrument calibration, or contamination
introduced during filtration) before proceeding
with any sample analyses. Reestablish
statistical control by analyzing three blank
samples.
Repeat QCCS analysis.
Recalibrate and analyze QCCS.
Reanalyze all routine samples (including PE and
field replicate samples) analyzed since the last
acceptable QCCS measurement.

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Laboratory
Duplicate
Sample: (All
analyses)
One per batch
<30%
If results are below LRL:
Prepare and analyze split from different sample
(volume permitting). Review precision of QCCS
measurements for batch. Check preparation of
split sample. Qualify all samples in batch for
possible reanalysis.
    Phytoplankton Analysis:
    It is critical that prior to taking a small portion of the subsample, the sample be thoroughly mixed
    and macro or visible forms are evenly dispersed.  Specific quality control measures are listed in
    Table 5.3-10 for laboratory identification operations.
   Table 5.3-10.  Laboratory quality control samples: phytoplankton indicator.
 QC Sample Type
  (Analytes), and
    Description
  Frequency
    Acceptance
      Criteria
           Corrective Action
Independent
identification by
outside taxonomist
All uncertain
taxa
Uncertain
identifications to be
confirmed by expert
in particular taxa
Record both tentative and independent IDs
Use standard
taxonomic
references
For all
identifications
All keys and
references used
must be on
bibliography
prepared by another
laboratory
If other references desired, obtain
permission to use.
            5.3.7.
    Data Reporting, Review, and Management
   Checks made of the data in the process of review and verification are summarized in Table 5.3-
   11. Data reporting units and significant figures are given in Tables 5.3-12 and 5.3-13.

   Crews must check the label to ensure that all written information is complete and legible. A strip
   of clear packing tape will be placed over the label, covering it completely. The sample ID and
   volume filtered will be recorded on the Sample Collection Form.  The crew must verify that the
   volume recorded on the label matches the volume recorded on the Sample Collection Form and
   enter a flag code and provide comments on the Sample Collection Form if there are any
   problems in collecting the sample or if conditions occur that may affect sample integrity.  The
   chlorophyll filter will be stored in a 50-mL centrifuge tube wrapped in aluminum foil and frozen

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using dry ice or a portable freezer. The crew leader will recheck all forms and labels for
completeness and legibility.
Table 5.3-11.  Data validation quality control: water chemistry, chlorophyll a and
phytoplankton indicators.
Activity or Procedure
Range checks, summary statistics, and/or
exploratory data analysis (e.g., box and
whisker plots)
Review holding times
Review data from QA samples (laboratory PE
samples, and interlaboratory comparison
samples)
Phytoplankton: taxonomic "reasonableness"
checks
Requirements and Corrective Action
Correct reporting errors or qualify as
suspect or invalid.
Qualify value for additional review
Determine impact and possible limitations
on overall usability of data
Second or third identification by expert in
that taxon
Table 5.3-12.  Data reporting criteria: water chemistry indicator.
Measurement
Total phosphorus
Total nitrogen
Nitrate- Nitrite
Ammonia
Units
mg/L P
mg/LN
mg/L as N
mg/L as N
No.
Significant
Figures
3
3
3
3
Maximum No.
Decimal Places
3
2
2
2

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Table 5.3-13.  Data reporting criteria: chlorophyll-a indicator.


Measurement
Chlorophyll-a


Units
ug/L
No.
Significant
Figures
2

Maximum No.
Decimal Places
1
5.4.    Benthic Macrovinvertebrates
        5.4.1.
Introduction
Benthic invertebrates inhabit the sediment (infauna) or live on the bottom substrates or aquatic
vegetation (epifauna) of coastal areas. The response of benthic communities to various
stressors can often be used to determine types of stressors and to monitor trends (Klemm et al.,
1990). The overall objectives of the benthic macroinvertebrate indicators are to detect stresses
on community structure in National coastal waters and to assess and monitor the relative
severity of those stresses. The benthic macroinvertebrate indicator procedures are based on
various recent bioassessment litrature (Barbour et al. 1999, Hawkins et al. 2000, Klemm et al.
2003) and previous coastal surveys (US EPA 2001C, US EPA 2004A, US EPA 2008).
        5.4.2.
Sampling Design
If unsuccessful in sediment collection, i.e, the substrate is too rocky, the crew will move into a
37 m buffer zone and retry. If the crew is still unsuccessful, the crew will move into a 100 m
buffer zone and attempt to collect sediments. For Great lakes sites only, a third attempt may be
made within a 500 m buffer zone if no sediment is collected. Any size sediment can be used for
the benthic macroinvertebrate sample. See Field Operations Manual (EPA, 201OA) for more
specifics.

The sediment grabs, taken from each station, will be sieved on site through a 0.5 mm mesh
sieve (1.0 mm mesh in CA, OR, WA) screen to collect macrobenthic infaunal organisms for
community structure assessments. The samples from each sieve will be preserved separately in
10% buffered formalin with Rose Bengal  vital stain to await later laboratory sorting,
identifications, and counts.

        5.4.3.       Sampling and Analytical Methods

Sample Collection:

A Van Veen sampler or Ponar dredge will be used to collect sediment samples. The depth of
sediment in the sampler should be >7 cm and the surficial sediment should still be present. If
the sample meets acceptability criteria, as detailed in the field operations manual, the first
sediment grab will be used as the benthic macroinvertebrate sample.  Descriptive information
about the grab, such as the presence or absence of a surface floe, color and smell of surface
sediments, and visible fauna will be included on the data sheet.

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Samples are field-processed; sieved to remove silty sediment, and large rocks or debris are
rinsed, inspected for organisms and removed. The remaining sample is gently rinsed to one
side of the sieve and carefully transferred into (a) 1 L bottle(s), such that the sample does not fill
the bottle to more than half-full. Samples will not be power rinsed as many of the polychaetes
(and other organisms) are very susceptible to losing their identifying characteristics when
handled too much or with too powerful of a rinse. The sample is then preserved with 10%
buffered formalin. Buffered formalin samples must be shipped via ground transport.  If samples
must be shipped  by air, the shipper must be trained  as a current HazMat shipper and complete
the appropriate paperwork.

Analysis:

Prior to beginning the analysis, EPA and benthic labs will ensure that appropriate keys are
being used by each lab and that all labs clearly understand and are using the same hierarchical
targets. Preserved composite samples are sorted (including possibly sub-sampling),
enumerated, and invertebrates identified to the species level, or lowest practical identifiable
level,  using specified standard keys and references. Processing and  archival methods are
based on standard practices. Detailed procedures are contained in the laboratory methods
manual and cited references. There is no maximum  holding time associated with preserved
benthic macroinvertebrate samples. All organisms will be sorted, counted and identified as
described in the lab manual.  A 10%  external check is standard QA for NCCA. For operational
purposes of the NCCA, laboratory sample processing should be completed by March 2011.
Table 5.4-1 summarizes field and analytical methods for the benthic macroinvertebrates
indicator.
        5.4.4.
Quality Assurance Objectives
MQOs are given in Table 5.4-1. General requirements for comparability and representativeness
are addressed in Section 2. The MQOs represent the maximum allowable criteria for statistical
control purposes. Precision is calculated as percent efficiency, estimated from examination of
randomly selected sample residuals by a second analyst and independent identifications of
organisms in randomly selected samples. The MQO for picking accuracy is estimated from
examinations (repicks) of randomly selected residues by experienced taxonomists.
Table 5.4-1. Measurement data quality objectives: benthic indicator.
Variable or
Measurement
Sort and Pick
Identification
Precision
90%
90%
Accuracy
90%
90%a
Completeness
99%
99%
 NA = not applicable

aTaxonomic accuracy, as calculated using Equation 10 in Section 2.

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The completeness objectives are established for each measurement per site type (e.g.,
probability sites, revisit sites, etc.). Failure to achieve the minimum requirements for a particular
site type results in regional population estimates having wider confidence intervals. Failure to
achieve requirements for repeat and annual revisit samples reduces the precision of estimates
of index period and annual variance components, and may impact the representativeness of
these estimates because of possible bias in the set of measurements obtained.
        5.4.5.
Quality Control Procedures: Field Operations
Prior to transferring sample to the bottle, the inner and outer sample bottle labels are checked to
ensure that all written information is complete and legible and the outer label is taped to the
sample bottle.  A flag code will be entered and comments provided on the Sample Collection
Form if there are any problems in collecting the sample or if conditions occur that may  affect
sample integrity.  Specific quality control measures are listed in Table 5.4-2 for field operations.
Table 5.4-2. Sample collection and field processing quality control: benthic
indicator.
Quality Control
Activity
Check integrity of
sample containers and
labels
Sample Processing
(field)
Sample Storage (field)
Holding time
Description and Requirements
Clean, intact containers and labels
Use 0.5 mm mesh sieve (1.0 mm mesh in CA,
OR, WA). Preserve with ten percent buffered
formalin. Fill jars no more than 1/2 full of
material to reduce the chance of organisms
being damaged.
Store benthic samples in a cool, dark place until
shipment to analytical lab
Preserved samples can be stored indefinitely;
periodically check jars and change the ethanol if
sample material appears to be degrading.
Corrective Action
Obtain replacement
supplies
Discard and
recollect sample
Discard and
recollect sample
Change ethanol
        5.4.6.
Quality Control Procedures: Laboratory Operations
     5.4.6.1.  Sample Receipt and Processing

Laboratory procedures and prescribed QA/QC requirements for benthic sample processing will
be based on those described in the NCCA Laboratory Methods Manual (EPA, 201 OB). The
samples should be stored in a dry, cool area and away from direct sunlight. The field preserved

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samples should be transferred to 70% ethanol within 2 weeks of collection. QC activities
associated with sample receipt and processing are presented in Table 5.4-3.
Table 5.4-3.  Sample receipt and processing quality control: benthic
macroinvertebrate indicator.
Quality Control
Activity
Sample Log-in
Sample Storage
Holding time
Preservation
Description and Requirements
Upon receipt of a sample shipment, laboratory
personnel check the condition and
identification of each sample against the
sample tracking record.
Store benthic samples in a cool, dark place.
Preserved samples can be stored indefinitely;
periodically check jars and change the ethanol
if sample material appears to be degrading.
Transfer storage to 70% ethanol.
Corrective Action
Discrepancies, damaged, or
missing samples are reported
to the IM staff and indicator
lead
Qualify sample as suspect for
all analyses
Qualify samples
Qualify samples
     5.4.6.2. Analysis of Samples

A fairly regimented process of QC checks has been developed and widely adopted by most
benthic ecology laboratories. The first five samples, sorted by each technician, will be re-
checked (major taxon groups separated from debris) by a senior sorting technician before
additional samples are processed.  Throughout theperiod of the project, a series random checks
of sorted samples, at least one of every ten samples processed by each technician is also
verified. The re-sorts will be conducted  on a regular basis on batches of 10 samples. The quality
criteria for the benthic sorting are that the QCed sorts from a technician's work be evaluated at
> 90% efficiency; that is the minimum level of acceptability,  in most instances without undue
complications (e.g., excessive detritus), the sorting efficiency should run  >95%. Sorting
efficiency (%) will  be calculated using the following formula:
       # organisms originally sorted
x100
# organisms originally sorted + additional # found in re-sort
If the QC work is substandard, all that technician's samples subsequent to the last passed
check must be re-sorted and the technician will be offered further instruction to correct the
deficiency. Only after the technician demonstrates to a senior technician that the problem has
been rectified, will he/she be allowed to process additional samples. Experience has shown that
in most situations of this nature, appropriate corrective measures are readily implemented and
that the work continues with little delay. Standard data forms will used to record the  results for
the original sorts and the QC re-sorts.

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Species identification, or identification to the lowest practical level and enumerations will be
performed by or under the close supervision of a senior taxonomist and only taxonomic
technicians with demonstrated ability will be allowed to assist in these tasks. Prior to any
sample processing, senior taxonomists from all benthic  laboratories participating in NCCA, will
agree upon procedures necessary to attain identification to the lowest practical level.  The first
five samples, counted and identified by each taxonomist, will be re-checked by a senior
taxonomist or a designated competent taxonomic technician, to verify accuracy of species
identification and enumerations, before work proceeds.  As with the sorting process,  at least one
out of every ten samples processed by each taxonomic technician will be also be re-checked  .
The QC check will consist of confirming identifications and recounting individuals of each taxon
group composing the sample. The total number of errors (either mis-IDs or miscounts)  will be
recorded and the overall percent accuracy will be computed using the following formula:

       Total # organisms in QC recount - total # or errors  x 100
       Total # of organisms in QC recount
The minimum acceptable taxonomic efficiency will be 90%. If the efficiency is greater than 95%,
no corrective action is required. However, if taxonomic efficiency is 90 - 95 %, the taxonomist
will be consulted and problem areas will be identified. Taxonomic efficiencies below 90% will
require re- identifying and enumerating all samples that comprised that batch. The taxonomist
must demonstrate an understanding of the problematic areas before continuing with  additional
samples, and then, his/ her performance will be closely monitored for sustained improvement.

In addition to the QC checks of taxonomist work, the QA program for benthic taxonomy requires
that the laboratory maintains a voucher collection of representative specimens of all species
identified in the NCCAbenthic samples. If possible, the collection should  have the identifications
verified by an outside source. The verified specimens should then become a part of the
laboratory's permanent reference collection which can be used in training new taxonomists.

NOTE:

Interlaboratory Calibration Exercise. Benthic community structure is a very critical element to the
overall assessment of the ecological condition of a coastal system. The procedures to sort and
correctly identify benthos are extremely tedious and require a high degree of expertise. Because
of benthos' importance to the study and the level of difficulty involved in processing, to evaluate
comparability among the laboratories, indicator lead and/or quality assurance project manager
may conduct interlaboratory calibration exercises in which replicate (or similar) benthic samples
will analyzed by the multiple laboratories involved.

Specific quality control measures are listed in Table 5.4-4 for laboratory operations. Figure 5.4.1
presents the general process for analyzing benthic invertebrate samples. Specific quality
control measures are listed in Table 5.4-5 for laboratory identification operations.

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Table 5.4-4. Laboratory Quality Control: benthic macroinvertebrate sample
processing.
Check or Sample
Description
Frequency
Acceptance Criteria
Corrective Action
SAMPLE PROCESSING (PICK AND SORT)
Sample residuals
examined by different
analyst within lab
Sorted samples sent to
independent lab
10% of all samples
completed per
analyst
10% of all samples
Efficiency of picking
>90%
Accuracy of contractor
laboratory picking and
identification >90%
If <90%, examine all
residuals of samples by
that analyst and retrain
analyst
If picking accuracy <90%,
all samples in batch will be
reanalyzed by contractor
Table 5.4-5: Laboratory Quality Control: benthic macroin vertebrate taxonomic
identification.
Check or Sample
Description
Duplicate
identification by
different taxonomist
within lab
Independent
identification by
outside taxonomist
Use widely/commonly
excepted taxonomic
references
Prepare reference
collection
Frequency
10% of all samples
completed per
laboratory
All uncertain taxa
For all
identifications
Each new taxon
per laboratory
Acceptance Criteria
Efficiency >90%
Uncertain
identifications to be
confirmed by expert in
particular taxa
All keys and references
used must be on
bibliography prepared
by another laboratory
Complete reference
collection to be
maintained by each
individual laboratory
Corrective Action
If <90%, re-identify all
samples completed by that
taxonomist
Record both tentative and
independent IDs
If other references desired,
obtain permission to use
from Project QA Officer
Lab Manager periodically
reviews data and reference
collection to ensure
reference collection is
complete and identifications
are accurate

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        5.4.7.
Data Reporting, Review and Management
Checks made of the data in the process of review, verification, and validation are summarized in
Table 5.4-6.
Table 5.4-6: Data review, verification, and validation quality control: benthic
indicator.
Check Description
Taxonomic
"reasonableness"
checks
Frequency
All data
sheets
Acceptance Criteria
Genera known to occur in
given coastal conditions or
geographic area
Corrective Action
Second or third
identification by
expert in that taxon
A reference specimen collection is prepared as new taxa are encountered in samples. This
collection consists of preserved specimens in vials and mounted on slides and is provided to the
responsible EPA laboratory as part of the analytical laboratory contract requirements. The
reference collection is archived at the responsible EPA laboratory.
Sample residuals,  vials, and slides are archived by each laboratory until the NCCA Project
Leader has authorized, in writing, the disposition of samples. All raw data (including field data
forms and bench data recording sheets) are retained in an organized fashion indefinitely or until
written authorization for disposition has been received from the NCCA Project Leader.

Data validation and reconciliation:

10% of the samples will be re-identified and counted by an independent taxonomist provided by
EPA.  EPA and the independent taxonomist will randomly select the  samples that will be re-
identified.  If the MQOs are  not met or taxonomist questions arise, there will be a reconciliation
phone call between the independent taxonomist and the lab.  During the call, the taxonomists
will discuss identifications or other issues that differed between the original atomist and the
independent taxonomist. If the reconciliation phone call does not result in data meeting the
MQOs, a third taxonomist may be brought in to re-id the samples.
5.5.    Sedimentand Fish Sampling and Chemistry
        5.5.1.

Sediment:
Introduction
While the first sediment grab sample is processed for benthic species composition and
abundance, additional sediment grabs are collected for chemical analyses (organics/metals and
TOC), grain size determination, and for use in acute whole sediment toxicity tests. The number
of grabs needed may vary based on the sediment characteristics and the area of the opening of
the dredge. These grabs will be composited, mixed and split into four separate sample
containers. A minimum of 4L of sediment will be required for the sediment composite sample.
Crews may send in less sediment if limited amounts of sediment could be acquired from the

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site.  If insufficient sediment is provided to conduct a complete analytical procedure, the lab
should contact EPA to discuss what if anything can be completed.

Fish:

Fish collected as indicators of ecological contamination (Eco-fish) will be collected at all sites to
be analyzed for whole body concentrations of organic and inorganic contaminants. This will
also include the analysis and  reporting of lipid content, sample weight and percent moisture.
Results from these analyses will be used to help determine the ecological integrity of U.S.
coastal resources. Specimen  collection will be based on biogeographically specific "target
species" lists developed for each of the regional areas- Great Lakes, Northeast, Southeast,
Gulf, and West Coast (see Table 5.5-1). In the event that target species cannot be caught at a
site, then species of similar habit/habitat may be substituted.  All attempts should  be made to
collect the targeted species.

In the Great Lakes, additional fish composite samples will be collected, and  fillets from these
samples will be analyzed for concentrations of organic and inorganic contaminants.  The Great
Lakes Human Health  fish tissue indicator (HH-fish) will provide information on the distribution of
mercury,  perfluorinated compound (PFC), polybrominated diphenyl ether (PBDE), omega-3 fatty
acid, and pharmaceutical residues in fish species consumed by humans from coastal areas of
the Great Lakes Region (see  Table 5.5-2 for list of target species). Crews should attempt to
adhere to the lists of target and alternative species for  human health fish collection.  The human
health fish tissue indicator procedures are based on EPA's National Study of Chemical
Residues in Lake Fish Tissue (USEPA 2000a) and EPA's Guidance for Assessing Chemical
Contaminant Data for Use in Fish Advisories, Volume 1 (Third Edition) (USEPA 2000b).

        5.5.2.       Sampling  Design

Sediment Collection:

The search for soft sediment can be expanded to within 37 m to collect sediment. If no
sediment is found, crews can expand the area to within 100 m.  For Great Lakes sites only, if no
acceptable sediment grabs are achieved, the crew may move the attempt to within 500 meters
of the X site. See the Field Operations Manual (EPA, 201OA) for more information.  The
sample will be checked for  acceptability and multiple grabs will make up the 4 L sample required
for the composite sample.  Unlike the benthic sample, the depth of sediment in the dredge need
not be 7 cm, but surficial sediment must be present.

   •   Note: While the field crew should make every attempt to collect all samples, there will
       be some circumstances that will prevent this from happening. When an insufficient
       amount of sediment can be collected to complete all analyses, crews are to follow the
       guidelines below:
          o  Benthic sample should be collected.  Any sediment size is acceptable so long as
             the definition of a "successful grab" is met (Benthic Grab criteria).
          o  Sediment composite material of sand-sized sediment grain or smaller, should be
             collected.

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                    Since there may be cases where only a limited amount of sediment can
                    be acquired for the sediment chemistry, characterization, and toxicity
                    composite. In these cases, the outline below provides the expected
                    sample in order of preference:
                        •   Contaminants
                        •   TOC
                        •   Silt/Clay (Grain size)
                        •   Toxicity
Fish Collection:
Any reasonable method which represents the most efficient or best use of the available time on
station may be used to collect the needed specimens. Specimens collected should be identified
by common name and genus-species and the length measured (appropriate to the species).
This data along with the quantity sent for analysis should be recorded.  Minimum length for an
Eco-fish specimen is 4.0 cm with a preferred length of 10 - 40 cm. Up to 20 individuals should
be collected and sent for chemical analysis.  HH-fish specimens must consist  of a composite of
fish (i.e., five individuals of one predator species that will collectively provide greater than 500
grams of fillet tissue) from each site.

Field teams will consist of one experienced fisheries biologist and one field technician. The
experienced on-site fisheries biologist will select the most appropriate sampling equipment.
Accurate taxonomic identification is essential to prevent mixing of species within composites.
Five fish will be collected per composite at each site, all of which must be large enough to
provide sufficient tissue for analysis (i.e., 500 grams of fillets, collectively). Fish in each
composite must all be of the same species, satisfy legal requirements of harvestable size (or be
of consumable size if there are no harvest limits), and  be of similar size so that the smallest
individual in the composite is no less that 75% of the total  length of the largest individual. If the
recommended target species are unavailable, the on-site fisheries biologist will select an
alternative species (i.e., a predator species that is commonly consumed in the study area, with
specimens of harvestable or consumable size, and in sufficient numbers to yield a composite).

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Table 5.5-1. Recommended target species for whole body fish tissue collection
by specific biogeographical region.

Northeast
Southeast/
Gulf of
Mexico
West Coast
Family name
(etaluridae
Moronidae
Paralichthvtdae
PleyrGnectidae
Sciaenidae
Sparidae
Nephropoidea
Anldae
Paralichthytdae
S'Ciaenidae
Sparidae
Atfiennoosidae
Cottidae
Cynogiessidae
EmbiotocKtae
Gasterosteidae
Paralichthytdae
Pleunonectidae
Soiaenidae
Serranidae
Common name
White catfish
Channel catfish
White perch
Summer flounder
Winter fte-und-er
Gray weakfish
Scuc
Lobster
Hardhead sea catfish
Gaffiopsal sea catfish
Southern flounder
Gulf Bunde*
Summer flounder
Sand weakfish (or seatrout)
Spot croaker
Gray weakfish
Atlsndc croaker
Speckled Trout
Red Drum
Pinffeh
Topsmelt silverside
Pacific staghom sculpin
Saddleback sculpin
California torsguefish
Shiner perch
Striped sea perct^
Three-soined stickleback
Pacific -sanctdab
Speckled sand&ab
Caiifom^a feunder
Butler sole
English sole
S-ta^rv feunder
Pacific sand sole
White croaker
Spotted sand bass
Barred sand bass
Scientific name
Ameittnts catus
Ictalurus ounctatus
Afcror» amsricana
Pafatichtfavs dentatus
Pseudop^eitYW7ecf»S' amen:canus
Cyno2.dorr nsgafe
Stsnotomis cfirvsoDS
Hoirmms americanus
Ario®3$3 fefs
Bsgf& ,ma/7nu-2
ParaUchtttys teftosftgma
Par&tichthvs a^&'outta
Paralicfathvs d&ntatus
Gynosoiofl arenaraj'S
Leioslotmis xanthums
C'^nos.G©fT reaafe
yfcfDpcQoni'as un(3ulatu3
Cwosdan nefcut'osus
Sdaenops ocellaius
Lagodon rfiomboj'des
Atfoednops sffcnis
Leatocottus armstus
Olaoootius rimensis
Symphunis aiiic-audus
Cymatogaster aggregata
Efftbictoca /sferafe
Gasterosteus actileatus aculeatus
Cithariehthys sordidus
Q"ftar3bM#3ys s&'gmaeiis
ParsV/orirriys cslffornxzus
Isoosflia isol&pis
Paro£»/tfv's v&fulus
Ptatichthys steiahis
Ps&ttkzhtfr/s m&tanostictus
Genyonemus lineatus
Paralabrax macvtatofsseistus
Parslabrax n&bulifer

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Lake
Erie
Lake
Huron
Lake
Superior
Lake Ontario
Lake
Michigan
Family name
Cjpriredae
Gobiidae
Idal uridae
Moronidae
Percidae
Sdaenndae
CerstrarcNdae
Cotbdae
Perddae
Osmeridae
Salmofiidas
C-atostOfTHdae
Cemrarchidae
Cctbdae
Cypriradaie
Esoadae
Gasterosteidae
Gobi-fdae
Ictaluridae
Lotidae
Moron ida&
Percidae
Pereopsidae
Saimonidae
Sesaeradae
Centrarcrsdae
Cotbdae
Cjpriredae
Gobitdae
Lotidae
Pereidae
Safrnonidae
Common name
Common carp
Round goby
Channel catfish
White perch
White bass
Yellow perch
Walleye
Freshwater drum
Smallmouth bass
Slimy 'seutpin
Yellow perch
Walleye
American / Rainbow smelt
Lak€ wtiitefish
Cisco / Lake Henir^i
Lake trout
Shorthead redhorse
Rook bass
Pdmpki-nseed
ffiuegil!
Smalimesuth bass
White crappie
Black eracwe
J»totfied sculpin
S4imy sciJpin
Common carp
Lake chub
Biunlnose mininow
Norttiem pike
Musheliunge
Three-spned sticWeback
Round gs*y
Tubenose goby
Brown bullhead
Stonecat
Channel catfish
Burbot
WNte perch
White bass
Ruffe
Yellow perch
Log perch
Sauger
Walleye
Trout-perch
Pink salmon
Coho salmon
Rainbow trout
Lake wfiitefish
Chinook salmon
Lake trout
Freshwater drum
Rock bass
Fxirnpkitseed
BluegiH
^totBed sculpir?
Slimy soulpin
Lake chub
BluRtnose 11 i re^cw
Round goby
Tuberose go&y
Burbot
Yellow perch
Log perch
Lake whitgfish
Lake trout
Scientific name
Cypn'nus carpki
WeogobttjB roe/armstorrus
Ict^ums pimctatus
Morons ameobaria
Morone ctirysops
Pe/ca flavescens
Sander vrtreus
ApkxSnotus gnruvens
Micropisrus dotomeu
Coitus ccgnsius
Perea ftaveacens
Sander vr'Sreus
Osments mordaif
Core^orajG c^ypeafemK's
Cofegonas Aft edf
Sa/i^inLfS rtamsyc^^
Afeicostoma macro/efN'abftjm
Ambtoplites nipestris
tepoira's gi'hbosus
Lefxxni's rnacrcchi'rLis
Mcrcpferus dotornieu
Pomoxis annularis
Pomoxis nigromaculatus
Coitus- bairdS
Coitus cognaSus
Cypnhijs carpto
Couesiu-s pfor?Aeos
Pimephalfs nctaius
ESOK JucVus
Esox masijtonoogy
Gasfefosfeus acuteatus actrfeatos
Necgobitis melariostomus
Protefortjrsos rnafmorafejs
Ameiunjs nebutosus
Ajlofan^^ ^svus
tefafuors punctatus
Lots iota
Mxone arrie/^cans
Afcrooe chryseps
G>ir7inoc€pr3afus ce/nuus
Beroa Sat-escera-
Peresna caprcdes
Sander canadenss
Sander vitrsus
Peraopsrs orwscomaycLe
Onoorfrynchus 'gcrfjuscrta
CncorffyncftuB tosuScri
Oncsrft>T!e'/)Lis rnyWss
Coregorajs a'upeaformrs
Onsorhynshus fshawytssha
Salvelinus namaycush
Apkdinotus gn^mrens
AmUopfffes Rjpestris
tepons's gr'fa&osus
leporres macrochi'njs
CofiuE bairdii
Coitus cognatus
Couesius plumbeus
Pimepfiales notatus
Neogobivs metanosiomtts
Pro^wonhy'nws msnnarBhjs
Lota lota
Peroa fevescer^s
PeK-itia caprodes
Coregonus rfupeafcmnjs
Sa/velrnu-3 namayoKft

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Table 5.5-2 Target Fish Species for Great Lakes HH fish tissue composites.
Priority Target Fish Species
Family Name
Centrarchktae
Cyprmidtie
EsockJae
Ictalundae
Lotidao
Mcrcnidaa
Percidae
Saimoisdae
Scuenidae

Family Name
it Atlililit-
I I'ltWihltXll
ictaiundM
Saltraitdaa
Common Name
Rock bws
SinaHroutli boss
Lai geroulh bass
1* 11't-iMpl.k1
fcl»t> I'M"
' '«nn tin CT|
Northern pike
Muskelunge
Chan pickerel
Channel catfish
Burbot
While perch
White bass
Yeiio.v perch
Sai.Kie
W-llhfr
l-ik"iv|iHish
'lift ;f ilium
'.'ollOidlllWl
' hii *t Lj)nH/i
Rfint**1. trail
At/onk salmon
Brwn trait
Lake fait
FrcshnvScf drum
Alternative Fish S
COItUHOn mHIB
OuillteCk
Longnose sucka
', 'llIPiUlkH
N'ltlMI SlHl'-I^H
BlIitlKll ll ff J
H * ( m ' tli)
11(1*1 j-in'i'-h
I u upl-in1-"^1
V/jtmirh
eh -c J
Longear sunfish
Blac* bullhead
Yellav bullhead
Brawi bullhead
Cisco
BIftllaf
Round whitedsh
Biook trow!
StientillcNanw
Amhtopfoes rupestis
MKi'tytemsitiwmi
AfcroptOTB salnwides
Ft, •! di \ (n v
P-;* >" ,,] fVt&ipJ
! ,, |>L|' f/ .1
fsox tea/s
&o.< /najquwongy
f sox wger
tte'trvtrj pjficteftf!
Lofa to(a
t'lo'WK arnsKuns
Mows ctoysqps
Perca fevescafs
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Oncorirynctius gorbuscto
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Anenw/s nelxiiKus
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Coregorws i'wyv
Piosopvin cyMroKiim
Sokelmis fcfltviate

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        5.5.3.       Sampling and Analytical Methods

Sediment Collection:

The number of Van Veen or Ponar grabs required to yield an adequate volume of composited
sediment will vary; however, surficial sediment from a minimum of three grabs should be
composited for the final sample.  Surficial sediment from the individual grabs will  be combined in
a clean, high-grade stainless steel or Teflon vessel. Between grabs, the composite will be held
on ice and covered to protect the sample from contamination (e.g., fuel or combustion
products). Each addition of sediment will be mixed in the composite bucket and the final mixture
will be stirred well to homogenize prior to sub-sampling.

Each grab sample will be inspected to ensure adherence to the criteria found in the Field
Operations Manual (EPA, 201OA) before any sample is added to the composite.  Once it has
been determined that there was no loss of surficial sediment and all criteria are met the top two
to three cm of sample will be collected with a stainless steel spoon and placed in the composite
bucket.  The sample in direct contact with the sides of the dredge is not collected, and contact
between spoon and dredge should be minimal.

Approximately 250 ml of the composite will be placed  in a clean, prelabeled, 500 ml glass wide-
mouth jar for organic and inorganic chemistry. The samples will be held on wet ice until transfer
to lab, within seven days of collection, where the samples should be frozen to await processing.
Fish Collection:
To provide samples for the analyses of chemical contaminants, attempts will be made to collect
fish by any reasonable method, representing the most efficient use of available time.  Methods
might include trawl, trap, seine, cast net  or hook and line. All fish/shellfish collected for tissue
analysis will  be identified to species and  recorded, with lengths, on the appropriate data sheet.
The list of the target species for Eco-fish is in Table 5.5-1 and for HH-fish is in Table 5.5-2.

EPA will provide fish tissue sample packing and shipping supplies (with the exception of dry
ice).  A list of equipment and expendable supplies is provided in the NCCA  Field  Operations
Manual (EPA, 2010A).

Eco-fish:

At sites where target species are captured  in sufficient numbers, five to ten  individuals of the
same species, with a length of 100 to 400 mm, will be combined into a composite sample of
approximately 500 g. The fish will first be measured and recorded on the sampling form, then
rinsed with site water, and bagged together with a sample identification label. The sample is
double-bagged, the bag is sealed with a  labeled zip-tie and the sample is frozen to await
shipping.
HH-fish:

Five fish, each from the human health target list will be individually wrapped in extra heavy-duty
aluminum foil.  Each foil-wrapped fish and will be placed into waterproof plastic tubing that will
be cut to fit the specimen (i.e., heavy duty food grade  polyethylene tubing provided by EPA),
and each end of the tubing will be sealed with a plastic cable tie.  A sample label will be taped
onto the outside of the tubing and all five individually-wrapped specimens from the site will  be
placed in a large plastic composite bag and sealed with a cable tie tagged with another sample
identification label.  These samples  are also frozen to await shipping.

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Sediment and Fish Tissue Analysis:
HH-fish: Please note: this QAPP covers the process of collecting and shipping fish for Human
Health analysis. EPA's OST is developing a separate QAPP and SOPs appropriate for the
analysis of these samples. Fish  composites for the HH indicator will remain frozen at the lab
until such time as that QAPP is completed and approved.

Eco-fish: Samples collected will  be analyzed for a variety of inorganic and organic
contaminants.  Lists of analytes can be found in Tables 5.5-3 through 5.5-7.  Lipid, total sample
weight and percent moisture will  also be reported.

Table 5.5-3.  Indicator List of Metals (sediment and eco-fish tissue).

            Aluminum
            Antimony (sediment only)
            Arsenic
            Cadmium
            Chromium
            Copper
            Iron
            Lead
            Manganese (sediment only)
            Mercury (analyzed for HH-fish tissue also)
            Nickel
            Selenium
            Silver
            Tin
            Zinc

Table 5.5-4.  Indicator List of Organchlorine Pesticides (sediment and eco-fish
tissue).
Compound
Aldrin
Y-BHC (Lindane)
a-Chlordane
2,4'-DDD
4,4'-DDD
2,4'-DDE
4,4'-DDE
2,4'-DDT
4,4'-DDT
Dieldrin
Endosulfan I
Endosulfan II
Endosulfan sulfate
Endrin
Heptachlor
Heptachlor epoxide
Hexachloro benzene
Mi rex
Toxaphene
trans-Nonachlor
Chemical Abstract Service (CAS)
Registry No.
309-00-2
58-89-9
5103-71-9
53-19-0
72-54-8
3424-82-6
72-55-9
789-02-6
50-29-3
60-57-1
959-98-8
33213-65-9
1031-07-8
72-20-8
76-44-8
1024-57-3
118-74-1
2385-85-5
8000-35-2
39765-80-5

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 Table 5.5-5.  Indicator List of PCBs (sediment and eco-fish tissue).
Compound
IUPAC(PCB)No.
2,4'-Dichlorobiphenyl
2,2',5-Trichlorobiphenyl
2,4,4'-Trichlorobiphenyl
2,2',3,5'-Tetrachlorobiphenyl
2,2',5,5'-Tetrachlorobiphenyl
2,3',4,4'-Tetrachlorobiphenyl
3,3',4,4'-Tetrachlorobiphenyl
2,2',4,5,5'-Pentachlorobiphenyl
2,3,3',4,4'-Pentachlorobiphenyl
2,3,3',4',6-Pentachlorobiphenyl
2,3,4,4',5- Pentachlorobiphenyl
3,3,4,4',5- Pentachlorobiphenyl
2,2',3,3',4,4'-Hexachlorobiphenyl
2,2',3,4,4',5'-Hexachlorobiphenyl
2,2',4,4',5,5'-Hexachlorobiphenyl
2,2',3,3',4,4',5-Heptachlorobiphenyl
2,2',3,4,4',5,5'-Heptachlorobiphenyl
2,2',3,4',5,5',6-Heptachlorobiphenyl
2,2',3,3',4,4',5,6-Octachlorobiphenyl
2,2',3,3',4,4',5,5',6-Nonachlorobiphenyl
2,2',3,3',4,4',5,5',6,6'-Decachlorobiphenyl
       Chemical Abstract
Service (CAS) Registry No.
              8                   34883-43-7
              18                  37680-65-2
              28                  7012-37-5
              44                  41464-39-5
              52                  35693-99-3
              66                  32598-10-0
              77                  32598-13-3
              101                 37680-73-2
              105                 32598-14-4
              110                 38380-03-9
              118                 31508-00-6
              126                 57465-28-8
              128                 38380-07-3
              138                 35065-28-2
              153                 35065-27-1
              170                 35065-30-6
              180                 35065-29-3
              187                 52663-68-0
              195                 52663-78-2
              206                 40486-72-9
              209                 2051-24-3
Table 5.5-6.   Indicator List of PAHs (sediment only).
                        Compound

                 Acenaphthene
                 Acenaphthylene
                 Anthracene
                 Benz(a)anthracene
                 Benzo(b)fluoranthene
                 Benzo(e)pyrene
                 Benzo(k)fluoranthene
                 Benzo(g,h,i)perylene
                 Benzo(a)pyrene
                 Biphenyl
                 Chrysene
                 Dibenz(a,Ji)anthracene
                 Dibenzothiophene
                 2,6-dimethylnaphthalene
                 Fluoranthene
           Chemical Abstract Service
              (CAS) Registry No.
         83-32-9
         208-96-8
         120-12-7
         56-55-3
         205-99-2
         192-97-2
         207-08-9
         191-24-2
         50-32-8
         92-52-4
         218-01-09
         53-70-3
         132-65-0
         581-42-0
         206-44-0

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                 Fluorene                 86-73-7
                 lndeno(1,2,3-c,d)pyrene     193-39-5
                 1-methylnaphthalene        90-12-9
                 2-methylnaphthalene        91-57-6
                 1-methylphenanthrene      832-69-9
                 Naphthalene              91-20-3
                 Perylene                 77392-71-3
                 Phenanthrene             85-01-8
                 Pyrene                   129-00-0
                 2,3,5-trimethylnaphthalene   2245-38-7
Table 5.5-7.  Indicator List for Human Health Fish Tissue Only (See HH-fish
tissue QAPP for more on these analytes).

      PBDEs
      PFCs
      Omega 3 fatty acids
      Pharmaceuticals
        5.5.4.
Quality Assurance Objectives
The relevant quality objectives for fish tissue sample collection activities are primarily related to
sample handling issues. Types of field sampling data needed for the sediment and fish tissue
indicator are listed in Table 5.5-8. Methods and procedures described in this QAPP and the
NCCA Field Operations Manual (EPA, 201OA) are intended to reduce the magnitude of the
sources of uncertainty (and their frequency of occurrence) by applying:

•     standardized sample collection and handling procedures, and
•     use of trained scientists to perform the sample collection and handling activities.
Table 5.5-8. Field Data Types: Sediment and Fish Tissue Indicators.
Variable or Measurement
Sediment jar
Fish specimen
Fish length
Composite classification
Specimen count classification
Measurement Endpoint or
Unit
Sample identification number
Species-level taxonomic identification
Millimeters (mm), total length
Composite identification number
Specimen number

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MQOs are given in Table 5.5-9. General requirements for comparability and representativeness
are addressed in Section 2.  The MQOs represent the maximum allowable criteria for statistical
control purposes. Target MDLs are listed in Table 5.5-10.


Table 5.5-9. Measurement quality objectives for fish tissue and sediment
indicators.
                                                   Maximum
                            Maximum Allowable     Allowable
                              Accuracy (Bias)       Precision      Completeness
     Indicator/Data Type          Goal (%D)        Goal (%RSD)        Goal
  Sediment contaminant analvses:
  Organics                         35%               30%             95%
  Inorganics                        20%               30%             95%

  Fish Tissue Analysis:

  Inorganics                        35%               30%             95%

  Organics                         20%               30%             95%
Accuracy (bias) goals are expressed either as absolute difference (± value) or percent deviation
from the "true" value; precision goals are expressed as relative percent difference (RPD) or
relative standard deviation (RSD) between two or more replicate measurements. Completeness
goal is the percentage of expected results that are obtained successfully.
Table 5.5-10 summarizes performance requirements for sediment and fish tissue chemistry
analytical methods. Analytical methods are based on EPA-validated methods.

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Table 5.5-10.  Target MDLs for laboratory analyses of NCCA samples.
                                   INORGANICS

                                   Eco-Fish Tissue             Sediments
                               (wet weight ug/g (ppm))   (dry weight ug/g (ppm))
    Aluminum                            10.0                    1500
    Antimony                        Not measured                 0.2
    Arsenic                               2.0                      1.5
    Cadmium                             0.2                     0.05
    Chromium                             0.1                      5.0
    Copper                               5.0                      5.0
    Iron                                 50.0                     500
    Lead                                 0.1                      1.0
    Manganese                      Not measured                 1.0
    Mercury                             0.01                     0.01
    Nickel                                0.5                      1.0
    Selenium                             1.0                      0.1
    Tin                                 0.05                     0.1
    Zinc                                50.0                     2.0


                                    ORGANICS
                                   Eco-Fish Tissue             Sediments
                               (wet weight ng/g (ppb))   (dry weight ng/g (ppb))

    PAHs                                NA                      10
    PCB congeners                        2.0                      1.0
    Chlorinated pesticides/DDTs             2.0                      1.0
    TOC                            Not measured                 100
        5.5.5.      Quality Control Procedures: Field Operations


Sediment Collection:
Any contamination of the samples can produce significant errors in the resulting interpretation.
Great care must be taken by the samplers not to contaminate the sediment with the tools used
to collect the sample (i.e., the dredge, spoons, mixing bucket) and not to mix the surface layer
with the deeper sediments. Prior to sampling, the dredge and collection tools that will come into
contact with the sediment must be cleaned with Alconox and rinsed with ambient water at the
site.  Field processing quality control requirements can be found in Table 5.5-11.

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Table 5.5-11. Sample collection and field processing quality control: sediment
chemistry indicator.
Quality Control Activity
Check integrity of sample
containers and labels
Sample Storage (field)
Holding time
Description and Requirements
Clean, intact containers and labels
Store sediment samples on wet ice and
in a dark place (cooler)
Refrigerated samples must be shipped
on wet ice within 1 week of collection
Corrective Action
Obtain replacement
supplies
Discard and recollect
sample
Qualify samples
Fish Collection:

HH and Eco-Fish:

The QC guidelines for fish collections relate to the conduct of the trawl, the correct identification
of the catch, and to the processing and preservation of the various sample types. A successful
trawl requires that the net deploys with the doors upright and spread and that the net fishes on
bottom for a 10±2 min duration without interruption. The trawl data will be recorded on the trawl
Information Data Sheet.

All fish tissue sampling teams will be required to view the training materials, read the QAPP,
and verify that they understand the procedures and requirements. Specific quality control
measures are listed in Table 5.5-12 for field measurements and observations.
Table 5.5-12. Field quality control: fish tissue indicator.
Quality Control Activity
Check integrity of sample
containers and labels
Set up fishing equipment
Field Processing
Holding time
Sample Storage (field)
Description and Requirements
Clean, intact containers and labels
An experienced fisheries biologist sets up the
equipment. If results are poor, a different method
may be necessary.
The fisheries biologist will identify specimens in
the field using a standardized list of common and
scientific names (Table 5.5-1). A re-check will be
performed during processing.
Frozen samples must be shipped on dry ice
within 2 weeks of collection
Keep frozen and check integrity of sample
packaging.
Corrective Action
Obtain replacement
supplies
Note on field data sheet
Attempt to catch more fish
of the species of interest.
Qualify samples
Qualify sample as suspect
for all analyses

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        5.5.6.
Quality Control Procedures: Laboratory Operations
The following is a list of analyses to be performed for sediment and Eco-Fish tissue samples.
HH-fish analyses and related quality control information can be found in the HH-fish tissue
QAPP. Although the following is not a complete list, it will serve to indicate the degree of quality
expected for analytical standards used to calibrate and verify analytical instrumentation:

Analyses of chemical  contaminants (e.g., PCBs, chlorinated pesticides,  PAHs, and trace
metals) in sediments and tissue:

Organics - NIST calibration solutions and matrix-specific SRMs
Inorganics - NIST or Baker calibration solutions; NRCC reference materials
Analysis of TOC in sediment:
Certified reference materials such as NIST 1941 and 8704
       Instrumentation that may require periodic maintenance and calibration verification:
Analytical Balances - annual verification by service representative;
Analytical Instrumentation (ICPs, GCs, AAs, AutoAnalyzer, etc.) - as per need based on general
performance; service contracts recommended.

All other sampling gear and laboratory instrumentation will be maintained in good repair as per
manufacturer's recommendations or common sense to ensure proper function.
     5.5.6.1. Sample Receipt and Processing
QC activities associated with sample receipt and processing of sediment and Eco-Fish samples
are presented in Table 5.5-13.  Information about HH-fish sample receipt activities can be found
in the HH-Fish QAPP.
Table 5.5-13.  Sample receipt and processing quality control: sediment and fish
tissue chemistry samples.
Quality Control
Activity
Sample Log-in
Sample Storage
Holding Time
Preservation
Description and Requirements
Upon receipt of a sample shipment,
laboratory personnel check the condition
and identification of each sample against
the sample tracking record.
All samples: -20 °C
1 year
None
Corrective Action
Discrepancies, damaged, or
missing samples are reported
to the IM staff and indicator
lead
Qualify sample as suspect for
all analyses
Qualify samples
Qualify samples

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     5.5.6.2. Analysis of Samples

QC protocols are an integral part of all analytical procedures to ensure that the results are
reliable and the analytical stage of the measurement system is maintained in a state of
statistical control.  Information regarding QC sample requirements and corrective actions for
sediment and Eco-Fish tissue samples are summarized in Table 5.5-14.  QC protocols for HH-
Fish samples can  be found in the HH-Fish QAPP.
Table 5.5-14.  Laboratory QC protocols.
 QC Sample Type
  (Analytes), and
    Description
Frequency
Acceptance
  Criteria
             Corrective Action
Method Blank
Once per
day prior to
sample
analysis
Control
limits < LRL
Prepare and analyze new blank. Determine and
correct problem (e.g., reagent contamination,
instrument calibration, or contamination
introduced during filtration) before proceeding
with any sample analyses. Reestablish
statistical control by analyzing three blank
samples.
LCS or SRM
Once per
day
Control
limits for
recovery
cannot
exceed
100±20%
Repeat LCS analysis.
Recalibrate and analyze LCS.
Calibration QCCS:
Before and
after
sample
analyses
±10% or
method
criteria
Repeat QCCS analysis.
Recalibrate and analyze QCCS.
Reanalyze all routine samples (including PE
and field replicate samples) analyzed since the
last acceptable QCCS measurement.
Laboratory
Duplicate Sample or
Matrix Spike
Duplicate samples:
(All analyses)
One per
batch
<30%
If results are below LRL:
Prepare and analyze split from different sample
(volume permitting).  Review precision of QCCS
measurements for batch. Check preparation of
split sample. Qualify all samples in batch for
possible reanalysis.
Matrix spike
samples:
One per
batch
Control
limits for
recovery
cannot
exceed
100±20%
Select two additional samples and prepare
fortified subsamples.  Reanalyze all suspected
samples in batch by the method of standard
additions.  Prepare three subsamples
(unfortified, fortified with solution approximately
equal to the endogenous concentration, and
fortified with solution approximately twice the
endogenous concentration.

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        5.5.7.
Data Reporting, Review and Management
Checks, made of the data in the process of review, verification and validation, are summarized
in Tables 5.5-15 and 5.5-16. Data reporting units and significant figures are given in Table 5.5-
17.  Data validation information for HH-Fish tissue samples can be found in the HH-Fish QAPP.
Table 5.5-15 Data validation quality control: sediment composite.
Activity or Procedure
Range checks, summary statistics, and/or
exploratory data analysis (e.g., box and
whisker plots)
Review data from QA samples (laboratory PE
samples, and interlaboratory comparison
samples)
Requirements and Corrective Action
Correct reporting errors or qualify as suspect
or invalid.
Determine impact and possible limitations on
overall usability of data
Table 5.5-16. Data validation quality control: eco-fish tissue indicator.
Check
Description
Taxonomic
"reasonableness"
checks
Composite validity
check
75% rule
Frequency
All data sheets
All composites
All composites
Acceptance Criteria
General known to occur
in coastal waters or
geographic area
Each composite sample
must have 5 fish of the
same species
Length of smallest fish
in the composite must
be at least 75% of the
length of the longest
fish.
Corrective Action
Second or third identification
by expert in that taxon
Indicator lead will review
composite data and advise the
lab before processing begins
Indicator lead will review
composite data and advise the
lab before processing begins

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Table 5.5-17 - Data Reporting Criteria: Sediment and Eco-Fish Tissue Chemistry.
Measurement
Units
Expressed to the
Nearest
Sediment and Fish Tissue:
Pesticides and PCBs
Metals
Hg
ng/g; ppb (sediment: dry wt and fish
tissue wet weight)
ug/g; ppm (sediment: dry wt and fish
tissue wet weight)
ug/g; ppm (sediment: dry wt and fish
tissue wet weight)
0.01
0.01
0.001
Sediment Only:
PAHs
ng/g; ppb (dry wt)
0.01
5.6.   Sediment Grain Size and TOC
        5.6.1.
Introduction
The physical properties of sediment including silt-clay content and TOC content will be
determined for sediment samples collected from each station.
        5.6.2.
Sampling Design
As discussed in Section 5.5, a composite sediment sample will be collected at the index site.
Using the stainless steel spoon, approximately 100 ml of sample will be transferred to a 125 ml
Nalgene bottle for grain size analysis and into a 60 ml Nalgene bottle for TOC analysis.

        5.6.3.       Sampling and Analytical Methods

Sediment Collection:

Enough surficial sediment will be collected from a minimum of three Van Veen or Ponar grabs to
produce a composite sample of approximately 4 L.  The acceptability criteria for each grab can
be found in the NCCA Field Operations Manual (EPA, 201OA).

TOC:

Sediment is placed in a 60 ml bottle for TOC analysis and kept on ice until reaching the
laboratory where it will be frozen to await further laboratory analysis. TOC will be determined by
combusting pre-acidified sediment samples in a TOC analyzer and measuring the volume of
CO2 gas produced.

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Grain Size:

Approximately 100 ml of composited sediment will be placed in a clean, prelabeled, 125 ml
Nalgene jar. The sample will be held on wet ice until it is transferred to the laboratory where it
will be refrigerated to await further laboratory processing.  Grain size will be determined by
using a 63 urn sieve for the separation of whole sediment into a large particle fraction
(sands/gravel) and fine particle fraction (silt-clays).
        5.6.4.
Quality Assurance Objectives
MQOs are given in Table 5.6-1.  General requirements for comparability and representativeness
are addressed in Section 2. The MQOs represent the maximum allowable criteria for statistical
control purposes.
Table 5.6-1. Measurement quality objectives for TOC and grain size indicators.


Indicator/Data Type
Particle Size
Total Organic Carbon
Maximum
Allowable
Accuracy (Bias)
Goal
NA
10%

Maximum Allowable
Precision
Goal
10%
10%


Completeness
Goal
95%
95%
Accuracy (bias) goals are expressed either as absolute difference (± value) or percent deviation
from the "true" value; precision goals are expressed as relative percent difference (RPD) or
relative standard deviation (RSD) between two or more replicate measurements. Completeness
goal is the percentage of expected results that are obtained successfully.
        5.6.5.
Quality Control Procedures: Field Operations
Error can be introduced during sampling activities and during field storage.  If samples are not
sufficiently homogenized or properly stored, inaccurate correlations may be drawn between the
physical characteristic results and the chemistry and toxicity results.  Field processing quality
control requirements can be found in Table 5.6-2.

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Table 5.6-2. Sample collection and field processing quality control: sediment
TOC and grain size indicator.
Quality Control
Activity
Check for homgeneity
Sample Storage (field)
Holding time
Check integrity of
sample containers and
labels
Description and Requirements
Sample must be homogenous
Store sediment samples on wet ice and in a
dark place (cooler)
Refrigerated samples must be shipped on
wet ice within 2 weeks of collection
Clean, intact containers and labels
Corrective Action
Mix sample for a longer
period of time
Discard and recollect
sample
Qualify samples
Obtain replacement
supplies
        5.6.6.
Quality Control Procedures: Laboratory Operations
Although the following is not a complete list, it will serve to indicate the degree of quality
expected for analytical standards used to calibrate and verify analytical instrumentation:

Analysis of TOC in sediment: Certified reference materials such as NIST 1941 and 8704
* CRMs, MESS-3 and PACS-2 distributed by the National Research Council of Canada's Marine
Analytical Chemistry Standards Program report total carbon concentrations of marine sediment
that are for information value only (they have no uncertainties associated with the values.

Instrumentation that may require periodic maintenance and calibration verification:

Analytical Balances -  annual verification by service representative;
Analytical Instrumentation (TOC Analyzer, etc.) - as per need based on general performance;
service contracts recommended.

An analytical balance accurate to 0.1 mg will be used for all weighings. Prior to each period of
use, the balance will be zeroed  and calibrated.  Its calibration will be verified using a standard
NIST weight; written documentation will be maintained.
     5.6.6.1.  Sample Receipt and Processing

QC activities associated with sample receipt and processing are presented in Table 5.6-3.

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Table 5.6-3.  Sample receipt and processing quality control: TOC and grain size
indicators.
Quality Control
Activity
Sample Log-in
Sample Storage
Holding Time
Description and Requirements
Upon receipt of a sample shipment, laboratory
personnel check the condition and
identification of each sample against the
sample tracking record.
TOC: Frozen -20°C, Grain size: refrigerate 4
°C
1 year
Corrective Action
Discrepancies, damaged, or
missing samples are reported
to the IM staff and indicator
lead
Qualify samples
Qualify samples
     5.6.6.2.  Analysis of Samples

Laboratory procedures for both analyses are based on those described in the NCCA Laboratory
Methods Manual (EPA, 201 OB). Methods for these analyses are relatively straightforward,
however, both include tedious procedures (e.g., precise sample weighing and pipetting) which
require strict attention to laboratory technique. Batch sizes for both should be < 25 samples.
Table 5.6-4 presents the QC guidelines specific for each analysis.

For grain size samples, within a given batch, the samples should be of similar textural
composition (i.e., either silty or sandy).  Sieves used for the grain size will have stainless steel
screens and they should be used exclusively for the grain size analysis; the sieves should be
cleaned with copious amounts of water and  brushes should not be used because they may
distort the openings. Two sediment fractions will be oven dried for 24 hrs, then weighed. To
ensure that the drying process had gone to completion, the weighed samples will be returned to
the drying oven for an additional 24 hrs and  randomly selected subsample is re-weighed as a
check for stability of the dry weights. All sample weighings will be recorded on preprinted data
sheets.

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Table 5.6-4.  Laboratory QC protocols for sediment TOC and grain size indicators.
QC Sample Type
(Analytes), and
Description
Laboratory/
Reagent Blank TOC
Laboratory
Duplicate Sample
TOC
CRM TOC
Grain Size Re-
analysis sample
Grain Size 2nd re-
analysis sample
Frequency
1 per batch of 20-25
samples
1 per batch of 20-25
samples
1 per batch of 20-25
samples
10%, but at least 2 samples
per batch must be
reanalyzed within 30 days of
initial analysis
10% of reanalyzed samples
must be reanalyzed by
second analyst within 30
days of initial analysis
Acceptance
Criteria
>10ppm
<10%
95-105%
<10%
<10%
Corrective Action
Re-analyze batch
Re-analyze batch
Re-analyze batch
Re-analyze batch
Re-analyze batch
        5.6.7.
Data Reporting, Review and Management
Checks made of the data in the process of review, verification, and validation are summarized in
Tables 5.6-5. Data reporting units and significant figures are given in Table 5.6-6.
Table 5.6-5 Data validation quality control: sediment TOC and grain size.
            Activity or Procedure
                         Requirements and Corrective Action
   Range checks, summary statistics, and/or
   exploratory data analysis (e.g., box and
   whisker plots)
                       Correct reporting errors or qualify as
                       suspect or invalid.
   Review data from QA samples (laboratory
   PE samples, and interlaboratory
   comparison samples)
                       Determine impact and possible limitations
                       on overall usability of data

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Table 5.6-6 - Data Reporting Criteria: Sediment Tests.
Measurement
TOC
Grain Size
Units
%
%
Expressed to the
Nearest
0.01
0.01
5.7.    Sediment Toxicity
        5.7.1.
Introduction
Toxicity tests will be completed on sediments from both marine/estuarine and freshwater
environments.  Both tests determine toxicity, in terms of survival rate of amphipod crustaceans,
in whole sediment samples.
        5.7.2.
Sampling Design
As discussed in Section 5.5, a composite sediment sample will be collected at the index site.
After the ~4 L of collected sediment has been homogenized and the chemistry, TOC and grain
size samples have been removed, the remainder (a minimum of three liters) of the sample is
placed in a one gallon plastic bucket and placed on wet ice.

        5.7.3.      Sampling and Analytical Methods

Sediment Collection:

Enough surficial sediment will be collected from a minimum of three Van Veen or Ponar grabs to
produce a composite sample of approximately 4 L. The acceptability criteria for each grab can
be found in the NCCA Field Operations Manual (EPA, 201OA).

Toxicity testing:

The sample will be held on wet ice until transport to the laboratory where it will be refrigerated at
4° C (sample is not to be frozen) to await further processing and initiation of testing within 30
days of collection. Sediment toxicity tests (SEDTOX) with amphipods will be conducted in
accord to the guidelines in the NCCA Laboratory Methods Manual (EPA, 201 OB); this method
describes test requirements and conditions in detail.
        5.7.4.
Quality Assurance Objectives
MQOs are given in Table 5.7-1.  General requirements for comparability and representativeness
are addressed in Section 2. The MQOs represent the maximum allowable criteria for statistical
control purposes.

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Table 5.7-1.  Measurement quality objectives for sediment toxicity indicator. Completeness
goal is the percentage of expected results that are obtained successfully.
Indicator/Data Type
Sediment toxicity
Maximum Allowable
Accuracy (Bias)
Goal
NA
Maximum Allowable
Precision
Goal
NA
Completeness
Goal
95%
        5.7.5.       Quality Control Procedures: Field Operations

Sediment Collection:

Any contamination of the samples can produce significant errors in the resulting interpretation.
Great care must be taken by the samplers not to contaminate the sediment with the tools used
to collect the sample (i.e., the dredge, spoons, mixing bucket) and not to mix the surface layer
with the deeper sediments.  Prior to sampling, the dredge and collection tools that will come into
contact with the sediment must be cleaned with Alconox and rinsed with ambient water at the
site.  Field processing quality control requirements can be found in Table 5.7-2.
Table 5.7-2. Sample collection and field processing quality control: sediment
toxicity indicator.
Quality Control
Activity
Check integrity of
sample containers and
labels
Sample Storage (field)
Holding time
Description and Requirements
Clean, intact containers and labels
Store sediment samples on wet ice and in a
dark place (cooler)
Refrigerated samples must be shipped on
wet ice within 2 weeks of collection
Corrective Action
Obtain replacement
supplies
Discard and recollect
sample
Qualify samples
        5.7.6.
Quality Control Procedures: Laboratory Operations
All laboratory instrumentation and equipment will be maintained in good repair as per
manufacturer's recommendations or common sense to ensure proper function. If not actual
calibration, all general laboratory equipment requires some documentation of performance.
Each piece of equipment should have an assigned logbook in which the calibration or
performance records are maintained.

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     5.7.6.1. Sample Receipt and Processing

QC activities associated with sample receipt and processing are presented in Table 5.7-3.
Table 5.7-3.  Sample receipt and processing quality control: sediment toxicity
indicator.
Quality Control
Activity
Sample Log-in
Sample Storage
Holding Time
Description and Requirements
Upon receipt of a sample shipment,
laboratory personnel check the
condition and identification of each
sample against the sample tracking
record.
All samples: 4 °C
30 days
Corrective Action
Discrepancies, damaged, or
missing samples are reported to
the IM staff and indicator lead
Qualify sample as suspect for all
analyses
Qualify samples
     5.7.6.2. Analysis of Samples

QC protocols are an integral part of all analytical procedures to ensure that the results are
reliable and the analytical stage of the measurement system is maintained in a state of
statistical control. Most of the QC procedures described here are detailed in the references for
specific methods. QC procedures pertain to two phases: pretest phase - initial demonstration of
technical ability; and, testing phase - daily monitoring of test conditions.
Initial Demonstration of Capability:

Before being authorized to conduct sedtox tests with NCCA sediments, a laboratory must
provide documentation of their technical capabilities by demonstrating that they have both the
facilities and personnel to meet the challenges to successfully conduct static toxicity tests for the
durations specified (i.e., 10-day exposures for amphipods).

If a laboratory has an established history of toxicity testing, then a review of their records may
be all that is required to ascertain their technical competence; examples of such records would
include current control charts for exposure of routine test species to reference toxicants, survival
rate for control organisms during recent test runs, and test organisms culturing/holding
logbooks.

On the other hand, if the laboratory is relatively unknown or newly organized, then it is highly
suggested that they first conduct a series of performance evaluation (PE) exercises prior to
being authorized to conduct toxicity test with NCCA sediments; also, a site visit to the testing

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facility is recommended to verify the laboratory's physical conditions. PE exercises should
include having the laboratory capture/culture or commercially obtain batches of approved test
species and hold them under the conditions described by test methods, without exposure to
toxic agents, to ensure that the laboratory technicians have the expertise required and that the
laboratory's systems are adequate to support the organisms in an apparent healthy state for the
designated period of testing (e.g., 10 days for marine amphipods). The laboratory should also
conduct a series of replicated exposures to reference toxicants to determine if the organisms
respond to the range of concentrations where effects are expected and to evaluate the
laboratory's degree of precision or reproducibility. Acceptability criteria for these PEs are for the
laboratory to demonstrate that they can successfully hold test organisms for up to 10 days with
survival rates of  >90%. For reference toxicant tests, the laboratory should produce calculated
LC50s (concentration estimated to be lethal to 50 percent of the organisms exposed to a test
treatment) within the range routinely reported by other testing laboratories with established
programs, and, the degree of precision between 4 or more replicated tests should be within a
range of 2 standard  deviations (2 sigma).

Evaluation should be made  by the EPA Project Officer. A laboratory should  not start testing with
NCCA sediments until notified in writing that they are qualified to initiate testing.

Daily Monitoring:

Tests will be conducted in accord to the procedures described in the NCCA Laboratory Methods
Manual (EPA, 201 OB). QC requirements during the test period include: daily checks of testing
conditions (e.g., dissolved oxygen concentration, temperature, and lighting)  and observations on
condition of test organisms.  These data will be checked on a daily basis and recorded on
standard data sheets as prescribed by the test method. Testing temperature should remain
within 20 ± 2 ° C; it can be measured from a beaker of water held in proximity to the test
chambers (e.g., in the water bath or temperature-controlled chamber) a recording temperature
gauge should be utilized. DO concentration should remain > 60% saturation; if the aeration
system malfunctions, the DO must be measured in all containers in which there was no aeration
(no visible bubbles from tube). Lighting will be constant (no night/day regime) for the duration of
the exposure period. For the test to be valid,  survival in the control  treatments must remain >
90% on average for the replicated control chambers, and no less than 85%  in any one
container.

        5.7.7.       Data Reporting, Review and Management

Checks made of the data in  the process of review, verification, and validation are summarized in
Tables 5.7-4. Data reporting units and significant figures are given  in Table 5.7-5.

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Table 5.7-4 Data validation quality control: sediment toxicity.
Activity or Procedure
Summary statistics, and/or exploratory
data analysis (e.g., box and whisker plots)
Review data from reference toxicity
samples
Requirements and Corrective Action
Correct reporting errors or qualify as
suspect or invalid.
Determine impact and possible limitations
on overall usability of data
Table 5.7-5 - Data Reporting Criteria: Sediment and Fish Tissue Chemistry.
Measurement
Sediment toxicity
Units
%
Expressed to the Nearest
Survival integer
5.8.    Pathogen Indicator
        5.8.1.
Introduction
The primary function of collecting water samples for Pathogen Indicator Testing is to provide a
relative comparison of fecal pollution indicators for national coastal waters. The concentration of
enterococci (the current bacterial indicator for fresh and marine waters) in a water body
correlates with the level of more infectious gastrointestinal pathogens present in the water body.
While some Enterococci are opportunistic pathogens among immuno-compromised human
individuals,  the presence of Enterococci is more importantly an indicator of the presence of
more pathogenic microbes (bacteria, viruses and protozoa) associated with human or animal
fecal waste. These pathogens can cause waterborne illness in bathers and other recreational
users through exposure or accidental ingestion. Disease outbreaks can occur in and around
beaches that become contaminated with high levels of pathogens. Therefore, measuring the
concentration of pathogens present in lake and pond water can help assess comparative human
health concerns regarding recreational use.

In this survey, a novel, Draft EPA Quantitative PCR Method 1606 (EPA, 2006A)will be used to
measure the concentration of genomic DMA from the fecal indicator group Enterococcus in the
water samples. While neither federal or state Water Quality Criteria (standards) have been
formally established for the level of Enterococcus DMA in a sample, epidemiological studies
(Wade et al. 2005) have established a strong  correlation between Enterococcus DMA levels and
the incidence of high-credible gastrointestinal illness (HCGI) among swimmers. The
Enterococcus qPCR results will serve as an estimate of the concentration of total (culturable
and non-culturable) Enterococci present in the surveyed coastal areas for the purpose of
comparative assessment. This study also has the potential to yield invaluable information about
the inhibitory effects of water matrices from the different regions of the nation upon the qPCR
assay.

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        5.8.2.
Sampling Design
A single "pathogen" water sample will be collected from the index site. The collection time of the
Enterococci sample may vary based on whether the team will be collecting fish for fish tissue
samples and whether those collections will be performed using an active or passive fishing
method. In short, if the team is not fishing, or is using a passive fishing method, the Enterococci
collection should take place immediately following the hydrographic profile. If the team is using
active fishing methods, the collection of the Enterococci sample should take place at the end of
the sampling day.  This is based on the need to protect the Enterococci sample from potential
contamination and to minimize holding times once the sample is collected.
        5.8.3.
Sampling and Analytical Methods
Sample Collection: The crews will collect a fecal indicator sample at the X-site. Using a pre-
sterilized, 250 ml bottle the sample will be collected at approximately 0.3 meter (12 inches)
below the water surface. For smaller vessels, this can be accomplished with a gloved hand. For
larger vessels, the bottle may need to be affixed to a pole dipper. Following collection, a sodium
thiosulfate tablet will be added, and the sample placed in a cooler, chill for at least 15 minutes.
Samples will remain on ice until four 50 ml_ volumes are filtered. (Samples must be filtered and
frozen on dry ice within 6 hours of collection). During sample collection the crew members will
look for signs of disturbance throughout the reach that would contribute to the presence of fecal
contamination to the waterbody and record these on the data sheet. Record these disturbances
on the Site Assessment Form (see Appendix B, NCCA Field Operations Manual (EPA, 201OA).

Analysis:

Pathogen samples are filter concentrated, then shipped on dry ice to the New England Regional
Laboratory where the filter retentates are processed, and the DMA extracts are analyzed using
qPCR, a genetic method that quantifies a DMA target via a fluorescently tagged probe, based
on methods developed by USEPA National Exposure Research Laboratory (EPA, 2006A).
Detailed procedures are contained in the laboratory operations  manual. Table 5.8-1  summarizes
field and analytical methods for the pathogen indicator.

Table  5.8-1. Field and laboratory methods: pathogen indicator (Enterococci).
Variable or
Measurement
Sample
Collection
Sub-sampling
QA
Class
C
N
Expected
Range and/
or Units
NA
NA
Summary of Method
Sterile sample bottle submerged to
collect 250-mL sample 6-12" below
surface at 10m from shore
2 x 50-mL sub-samples poured in
sterile 50-mL tube after mixing by
inversion 25 times.
References
NCCA Field Operations
Manual 2010 (EPA,
201 OA)
NCCA Laboratory
Methods Manual 2010
(EPA, 201 OB)

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Sub-sample
(& Buffer
Blank)
Filtration
Preservation &
Shipment
DMA Extraction
(Recovery)
Method 1606
(Enterococcus
& SPC qPCR)
N
C
C
C
NA
-40C to +40
C
10-141%
<60 (RL) to
>100,000
ENT CCEs
/100-mL
Up to 50-mL sub-sample filtered
through sterile polycarbonate filter.
Funnel rinsed with minimal amount of
buffer. Filter folded, inserted in tube
then frozen.
Batches of sample tubes shipped on
dry ice to lab for analysis.
Bead-beating of filter in buffer
containing Extraction Control (SPC)
DMA. DMA recovery measured
5-uL aliquots of sample extract are
analyzed by ENT & Sketa qPCR
assays along with blanks, calibrator
samples & standards. Field and lab
duplicates are analyzed at 10%
frequency. Field blanks analyzed at
end of testing only if significant
detections observed.
NCCA Laboratory
Methods Manual 2010
(EPA, 201 OB)
NCCA Laboratory
Methods Manual 2010
(EPA, 201 OB)
EPA Method 1606
Enterococcus qPCR
(EPA, 2006A)
EPA Draft Method 1606
Enterococcus qPCR
(EPA, 2006A)
NERL NLPS2007 qPCR
Analytical SOP (EPA,
2006A)
 C = critical, N = non-critical quality assurance classification.
        5.8.4.
Quality Assurance Objectives
MQOs are given in Table 5.8-2. General requirements for comparability and representativeness
are addressed in Section 2. Precision is calculated as percent efficiency, estimated from
independent identifications of organisms in randomly selected samples. The MQO for accuracy
is evaluated by having individual specimens representative of selected taxa identified by
recognized experts.
Table 5.8-2.  Measurement data quality objectives: Pathogen-Indicator DMA
Sequences.
Variable or Measurement*
SPC & ENT DNA sequence
numbers of Calibrators &
Standards by AQM
ENT CCEs by dCt ROM
ENT CCEs by ddCt ROM
Method Precision
RSD=50%
RSD = 70%
RSD = 70%
Method Accuracy
50%
35%
50%
Completeness
95%
95%
95%
*AQM = Absolute Quantitation Method; ROM = Relative Quantitation Method;
 SPC = Sample Processing Control  (Salmon DNA / Sketa); CCEs = Calibrator Cell Equivalent

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        5.8.5.
Quality Control Procedures: Field Operations
It is important that the sample container be completely sterilized and remains unopened until
samples are ready to be collected. Once the sample bottles are lowered to the desired depth (6-
12 in. below the surface), the sample bottles may then be opened and filled. After filling the 250-
ml_ bottle, a small portion of the sample should be discarded and the sodium thiosulfate tablet is
added to the sample for de-chlorination. Enter a flag code and provide comments on the
Sample Collection Form if there are any problems in collecting the sample or if conditions occur
that may affect sample integrity. All samples should be placed in coolers and maintained on ice
during the time interval before they are filtered for analysis. Samples must remain on ice a
minimum of 15 minutes prior to filtration.  Recheck all forms and  labels for completeness and
legibility.  Field blanks will be collected at 10% of sites sampled.

Specific quality control measures are listed in Table 5.8-3 for field measurements and
observations.

Table 5.8-3. Sample collection and field processing quality control: fecal indicator.
Quality Control
Activity
Check integrity of
sample containers and
labels
Sterility of sample
containers
Sample Collection
Sample holding
Field Processing
Field Blanks
Description and Requirements
Clean, intact containers and labels
Sample collection bottle and filtering apparatus
are sterile and must be unopened prior to
sampling. Nitrile gloves must be worn during
sampling and filtering
Collect sample after fishing to assure that
samples will be filtered within 6 hours
Sample is held in a cooler on wet ice until filtering
Sample is filtered and filters are frozen on dry ice
within 6 hours of collection
Field blanks must be filtered at 10% of sites
Corrective Action
Obtain replacement
supplies
Replace with sterile
supplies and re-
collect or re-filter
sample, as
appropriate
Re-collect
Re-collect
Qualify samples
Qualify samples
        5.8.6.       Quality Control Procedures: Laboratory Operations

Specific quality control measures are listed in Table 5.8-4 for laboratory operations

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Table 5.8-4. Laboratory Quality Control: Pathogen-Indicator DMA Sequences.
Check or
Sample
Description
Frequency
Acceptance Criteria
Corrective Action
SAM RLE PROCESSING
Re-process sub-
samples
(Lab Duplicates)
10% of all
samples
completed per
laboratory
Percent Congruence
<70% RSD
If >70%,
samples
re-process additional sub-
qPCR ANALYSIS
Duplicate analysis
by different
biologist within lab
Independent
analysis by
external
laboratory
Use single stock
of E. faecalis
calibrator
10% of all
samples
completed per
laboratory
None
For all qPCR
calibrator
samples for
quantitation
Percent Congruence
<70% RSD
Independent
analysis TBD
All calibrator sample
Cp (Ct) must have
an RSD < 50%.
If >70%,
cause is
samples
determine reason and if
systemic, re-analyze all
in question.
Determine if independent analysis
can be funded and conducted.
If calibrator Cp (Ct) values exceed
an RSD value of 50% a batch's
calibrator samples shall be re-
analyzed and replaced with new
calibrators to be processed and
analyzed if RSD not back within
range.
DATA PROCESSING & REVIEW
100% verification
and review of
qPCR data
All qPCR
amplification
traces, raw and
processed data
sheets
All final data will be checked
against raw data, exported
data, and calculated data
printouts before entry into LI MS
and upload to Corvallis, OR
database.
Second tier review by
contractor and third tier
review by EPA.

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     5.8.6.1.  Sample Receipt and Processing

Tubes are received on dry ice and may be frozen at -20° C or -70° C until analysis.
     5.8.6.2.  Analysis of Samples

There are involved laboratory quality control operations that must precede and accompany
sample analysis. See Section 3.6 of the NCCA Laboratory Quality Control Manual for a
description of each quality measure.
        5.8.7.
            Data Reporting, Review and Management
Checks made of the data in the process of review and verification are summarized in Table 5.8-
5.

Table 5.8-5. Data validation quality control: fecal indicator.	
     Check
   Description
             Frequency
 Acceptance Criteria
      Corrective Action
Field filter blanks
         Field blanks filtered
         at 10% of sites
Measurements should
be within 10 percent
Review data for
reasonableness; determine if
acceptance criteria need to be
modified
5.9.    Site Characteristics

Prior to leaving the area, the crew will fill out a field data sheet with information about the site
land use activities on the adjacent shoreline.  It also provides opportunity for crew members to
include their impression of biotic integrity, plant diversity and any anecdotal information provided
by locals.
  6.
FIELD AND BIOLOGICAL QUALITY EVALUATION & ASSISTANCE VISITS
 Procedural review and assistance personnel are trained to the specific implementation and data
collection methods detailed in the NCCA Field Operations Manual (EPA, 201OA).  Plans and
checklists for field evaluation and assistance visits have been developed to reinforce the
specific techniques and procedures for both field and laboratory applications.  The plans and
checklists are included in this section and describe the specific evaluation and corrective actions
procedures.

It is anticipated that evaluation and assistance visits will be conducted with each Field Team
early in the sampling and data collection process, and that corrective actions will be conducted

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in real time.  These visits provide a basis for the uniform evaluation of the data collection
techniques, and an opportunity to conduct procedural reviews as required to minimize data  loss
due to improper technique or interpretation of program guidance. Through  uniform training  of
field crews and review cycles conducted early in the data collection process, sampling variability
associated with specific implementation or interpretation of the protocols will be significantly
reduced. The field sampling evaluations, while performed by a number of different supporting
collaborator agencies and participants, will be based on the uniform training, plans, and
checklists.  This review and assistance task will be conducted for each crew collecting and
contributing data under this  program; hence no data will be recorded to the project database
that were produced by an 'unaudited' process, or individual.

Similarly, laboratory evaluation and assistance visits will be conducted early in the project
schedule and soon after sample processing begins at each laboratory to ensure that specific
laboratory techniques are implemented  consistently across the multiple laboratories generating
data for the program. Laboratory evaluation and assistance visit plans and checklists  have
been developed to ensure uniform interpretation and guidance in the procedural reviews.
These laboratory visits are designed such that full corrective action plans and remedies can be
implemented in the case of  unacceptable deviations from the documented procedures observed
in the review process without recollection of samples.

NCCA represents a  matrix of diverse environmental monitoring measurements and data
acquisition activities. Data quality criteria have been established for most of these
measurements and the QA  program will monitor the success rate of NCCA in meeting the
quality goals. While all of the data acquisition activities are of value to the project, certain  of
them have a higher degree  of import than others and will, therefore, receive priority regarding
review and assessment of the data quality,  especially in the more structured format of audits.
Nonetheless, for those activities that are not audited, there are sufficient QA/QC elements
associated with each data generating activity to enable the responsible analyst to make a
determination on the acceptability of the data. In most cases if the process fails QC checks, the
QA policy requires that the samples be re- analyzed until  acceptable data are attained. The
following sections outline the structured data reviews and assessments of data quality planned
for NCCA. Note, if situations warrant, any QA Coordinator delegated NCCA responsibilities  will
have authority to initiate an  audit or review of any NCCA environmental data collection activity
that fall under their purview. The States may also elect to initiate audits of their respective in-
house activities, at anytime.

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6.1    Field Quality Evaluation and Assistance Visit Plan for the NCCA

FIELD MONITORING

Field Crew Certification

Prior to the start of the 2010 field monitoring, each field crew will be required to complete a 3-4-
day field training to be authorized to collect actual NCCA field data and samples. Training will
consist primarily of hands-on sessions during which field crew members will be instructed by
the QA and Logistics specialists on the sampling methods and protocols developed for NCCA.
The training  for each crew will  culminate with an exercise in which crew members are observed
and evaluated as they perform the full suite of core field activities (i.e., complete sampling for a
NCCA site).  Although that is the preferred approach, because of time and logistical constraints,
it may be necessary to certify the crews as they master each major component (e.g., sediment
grabs for surficial sediment), then move on to the next, without observing in the context of a
real world situation. If a crew fails to qualify on some aspect, the members will receive further
instruction in the area of their deficiencies until they perform at an acceptable level.  The
training schedule can be found in section 1.2.1.

Field Reviews

A number of field teams will be responsible for the collection of environmental data and
samples from the NCCA sampling sites.. It is necessary to maintain an acceptable degree of
uniformity between the multiple groups conducting these tasks.  NCCA incorporates standard
protocols and guidelines to help ensure that the data collected are of known quality. These
guidelines allow for the use of different equipment (e.g.,  various hydrographic meters, work
vessels, etc.) as long as the data generated meet NCCA acceptability criteria. Such
performance-based QA/QC is  a key factor  to NCCA's success in  deriving comparable data
from diverse participants. Prior to the actual collection of NCCA field data, the field crews are
instructed in the approved field methods and protocols during their required initial training.

The format for the evaluations will be more of a field "surveillance review." than "audit." The
surveillance  reviews or audits will be conducted by appropriate NCCA Regional,  Headquarters,
ORD or contractor personnel. The goal is to conduct at least one review per crew early in the
crew's field season. The evaluator will meet the crew in the field and accompany them as they
conduct full-scale monitoring activities at one or more sampling sites. The evaluator will use an
approved NCCA checklist to systematically document acceptable/unacceptable performance on
all pertinent aspects of the sampling (see EPA Site Evaluation Guidelines document (EPA,
201OC)).


Any minor deficiencies observed during a field surveillance (e.g.,  slight deviation from approved
procedures,  labeling irregularities, data reporting, etc.) should be immediately pointed out to the
crew and corrective actions imposed on-the-spot. The evaluator will document with a brief note

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on the checklist and no further writeups are required. If significant deficiencies (i.e., data quality
is seriously compromised) are observed,  the evaluator will make the appropriate on-the-spot
correction, and, if the case warrants, call  a halt to the field activities until the problems are
resolved to the satisfaction of the QA Coordinator. All cases of this nature will be documented
through a written report submitted to the QA Coordinator.


Evaluators: One or more designated EPA or Contractor staff members who are qualified (i.e.,
have completed training) in the procedures of the NCCA field sampling operations.
To Evaluate: Field Sampling  Teams during sampling operations on site.

Purpose: To identify and correct deficiencies during field sampling operations.

1.  Maria Smith and Joe Hall will review the Field Evaluation and Assistance Visit Plan and
   Check List with each Evaluator during field operations training sessions.
2.  Maria Smith and Joe Hall will send a copy of the final Plan and the final Check List pages,
   NCCA QAPP and Field Operations Manual (EPA, 201OA) to each participating Evaluator.
3.  Each Evaluator is responsible for providing their own field gear sufficient to accompany the
   Field Sampling Teams (e.g., protective clothing, sunscreen, insect repellent, hat, water
   bottle, food, back pack, cell phone) during a complete sampling cycle. Schedule of the Field
   visits will be made by the Evaluator in consultation with the Maria Smith and the respective
   Field sampling crew Leader.  Evaluators should be prepared to spend additional time in  the
   field if needed (see below).
4.  Working with Maria Smith, EPA evaluators will arrange the schedule of visitation with each
   Field Team. When appropriate, Maria Smith will work with the contractor to schedule field
   audits.  Ideally, each Field Team will  be evaluated within the first two weeks of beginning
   sampling operations, so that procedures can be corrected or additional training provided, if
   needed.
5.  A  Field Team for the NCCA consists of a two- to four-person crew where, at a minimum, the
   Field sampling crew Leader is fully trained.
6.  The Evaluator will view the performance of a team through one complete set of sampling
   activities as detailed on the Field Evaluation and Assistance Check List.
   a.   Scheduling might necessitate starting the evaluation midway on the list of tasks at a site,
       instead of at the beginning.  In that case, the Evaluator will follow the team to the next
       site to complete the evaluation of  the first activities on the list.
   b.   If the Team misses or incorrectly performs a procedure, the Evaluator will note this on
       the checklist and immediately point this out so the mistake can be corrected on the spot.
       The role of the Evaluator is to provide additional training and guidance so that the
       procedures are being performed consistent with the Field Operations Manual (EPA,
       2010A), all data are recorded correctly, and paperwork is properly completed at the site.
   c.   When the sampling operation has been completed, the Evaluator will review the results
       of the evaluation with the  Field Team before leaving the site (if practicable), noting
       positive practices and problems (i.e., weaknesses [might affect data quality]; deficiencies
       [would adversely affect data quality]).  The Evaluator will ensure that the Team
       understands the findings and will be able to perform the procedures properly in the
       future.
   d.   The Evaluator will record responses or concerns, if any, on the Field Evaluation and

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       Assistance Check List. They will review this list with the field sampling crew at the site.
   e.  If the Evaluator's findings indicate that the Field Team is not performing the procedures
       correctly, safely, or thoroughly, the Evaluator must continue working with this Field Team
       until certain of the Team's ability to conduct the sampling properly so that data quality is
       not adversely affected.
   f.   If the Evaluator finds major deficiencies in the Field Team operations (e.g., less than two
       members, equipment or performance problems) the Evaluator must contact one of the
       following QA officials:
            i. Maria Smith (202-566-1047)
            ii. Joe Hall, EPA NCCA QA Officer (202-566-1241)
7.  The QA official will contact the EPA Project Leader (Gregory Colianni) or Alternate EPA
   Project Leader (Treda Grayson) to determine the appropriate course of action.
8.  Data records from sampling sites previously visited by this Field Team will be checked to
   determine whether any sampling sites must be redone.
9.  Complete the Field Evaluation and Assistance Check List,  including a brief summary of
   findings, and ensure that all Team  members  have read this and signed off before leaving the
   Team.
10. Make a copy of the Field Evaluation and Assistance Check List. Mail the original of each
   completed Laboratory Evaluation and Assistance Check List to Maria Smith whose address
   is in Table 1.2-1  in Section 1.
11. Maria Smith and Joe Hall will review the returned Field Evaluation and Assistance Check
   Lists, note any issues, check off the completion of the evaluation for each participating
   Laboratory. The original will be filed in the NCCA QA Officer file, Washington DC and pdf
   versions will be emailed to the appropriate lab, state  and regional contacts.

6.2.    Laboratory Quality Evaluation  and Assistance Visit Plan for the  NCCA

LABORATORY ACTIVITIES

Analytical Chemistry:

The analyses of chemical contaminants (organics and inorganics) in environmental samples are
the more difficult analytical activities within the project. NCCA has a vigorous performance
based QA/QC program to help ensure that data are of known and acceptable quality (see
Quality Control Procedures section for each indicator in Section 5 of this document for detailed
description). Because these analyses are technically challenging and  relatively expensive to
conduct, NCCA will require each analytical laboratory to  successfully complete an initial
demonstration of technical capability prior to being authorized  to conduct analyses with actual
NCCA samples.

First the laboratory must demonstrate that it is capable of meeting the target MDLs for each
analyte of interest in the matrices to be analyzed. Each laboratory must calculate and report
MDLs following the procedure specified in 40 CFR Part 136 (Federal Register, Oct. 28, 1984).
The matrix and the amount of sample used to determine MDLs should match as closely as
possible the matrix and amount of sample that will be used in the analyses of the field samples.

Laboratories can demonstrate the capability to conduct analyses  in multiple ways. They may
provide the results from an accredited  lab certification program (i.e. NELAC), audit results

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conducted from other projects, results from laboratory intercomparison studies, or choose to
analyze a blind evaluation sample.

Routine analyses of samples will be conducted in batch runs consisting of 25 or less field
samples along with a full complement of QC samples, typically including: continuing calibration
curves, reagent blanks, matrix spikes (MS) and MS duplicates, and a reference material
(either a SRM or a laboratory control material). These QC samples should be sufficient to
allow the analyst, on a real time basis, to evaluate the overall data quality of the sample batch;
please refer to the NCCA Laboratory Methods Manual (EPA, 201 OB) for a comprehensive
discussion of the performance-based QC philosophy and components. If the quality criteria
are not met, the analyst should take corrective actions and rerun the batch. When laboratories
adhere to this level of in-house data review, only batches that pass the general QC checks
should be submitted as final data to the NCCA.

Data reports submitted for to NCCA from analytical chemistry laboratories should include the
results of all required QC samples. These data will be thoroughly reviewed by NCCA personnel
to verify that the quality goals were satisfied. Analytical results that do not meet the general  QC
requirements will be identified in the NCCA data set with an appropriate QC code.

Laboratories conducting analyses are subject to audits at all phases of their association with the
project. The audits can be relatively informal site visits or technical systems audits (TSA)
conducted prior to, or early in, the project, primarily to confirm that the laboratory has
appropriate facilities, personnel, and resources required to conduct the analyses. A  more
formalized "audit of data quality" may be scheduled after the analyses are well underway or
completed, but not beyond a 2-year period of their completion. Audits of data quality are
formatted to determine if the QA/QC requirements outlined in the QAPP were in fact followed
and documented. If at all possible,  NCCA will conduct both TSAs and audits of data quality for
each analytical laboratory participating in the project. These audits will be announced well in
advance (no surprise audits). However, EPA retains the right to request periodic briefing on the
status of QA/QC or specific QC data at any time and if there is reason to suspect that the quality
standards are not being met, the NCCA management (i.e, Project Manager or QA Coordinator)
can suspend the analysis until the laboratory demonstrates the analytical process is back in
control.

Water Quality Analyses

This suite of analyses consists of separate laboratory determinations for several indices of
eutrophication conditions in water (e.g., soluble nutrient levels and chlorophyll content).
Although different methods and instrumentation are utilized for the specific measurements, all
are conducted using analytical systems that incorporate similar QC requirements (e.g., standard
curves, blanks, replicates, and spikes  or reference samples) on  a batch basis. The QC elements
provide the analyst with an immediate indicator of the data quality for a given batch of field
samples. If a batch run is substandard, the analyst should halt the analytical process until the
problem has been resolved. If the problem is straightforward, the analyst should make the
appropriate corrective actions, document the event, then continue or repeated the analysis.  If
the problem appears complex, for example - such that the entire data set is jeopardized,  then
the analyst (or laboratory) must inform the State or Regional QA Coordinator of the situation and
await further guidance before resuming with the analysis.

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The performance level for these analyses will be assessed during several stages of their
conduct. The laboratory must supply documentation that they can successfully conduct the
required analyses and meet the required QA. The EPA Project Officer must first approve the
overall performance for the analytical process before the laboratory (or analyst) is authorized to
proceed with the analysis of NCCA field samples. NCCA management personnel will attempt to
visit each group, firsthand, and observe the analyses while in progress. If at any time, NCCA
management is not satisfied that the quality standards are being met, the analysis may be
suspended until corrective measures are taken and the analysis is shown to be under control.
The data report submitted by each group should include all QA/QC results. An audit of data
quality may be conducted for any of the analytical activities within 2 years following their
completion.

Sediment Characterizations

Percent Silt-Clay:

Sediment grain size will  be characterized as percent silt-clay. The procedures, while tedious,
are basically a gravimetric determination. The primary QA governing this analysis is  strict
adherence to the methods described in the NCCA Laboratory Methods (EPA, 201 OB). The QC
checks for this activity involve replicate samples (10% of all  samples) as a check on precision;
there are no accuracy-based checks. If the QC replicate fails the quality criteria, the technician
will re-analyze all samples from the failed batch.

Before silt-clay determinations are conducted with actual NCCA samples, the laboratories slated
to perform the assays may be provided with a series of performance evaluation samples
representing the range of silt-clay expected in the CM sediments. An audit of data quality may
be conducted for this activity at anytime during a 2-year period following its completion.
TOC:

Sediment samples from each NCCA sampling station will be analyzed for TOC. These analyses
will be conducted by using a TOC analyzer; QC samples including carbon standards, blanks,
duplicate samples, and a SRM will be utilized on a per batch basis. Once the TOC analyzer is
calibrated, the analysis is relatively straightforward. Prior to the startup of actual NCCA sample
analysis, the analyst must demonstrate that the instrument is in calibration and producing
precise, accurate results for a certified reference material. The NCCA field samples should be
analyzed in batches of 25 or less samples; the analyst will review the results of the QC samples
upon the completion of the analytical run. If the quality criteria are not met, the batch will be re-
analyzed. Sediment TOC data is subject to an audit of data quality during the 2-year period
following the completion of the analysis.

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Benthic Community Assessment:
Sediment grabs will be collected from each NCCA station for evaluations of macrobenthic
infanual community structure. These types of benthic evaluations should only be undertaken by
experienced personnel with demonstrated competence in the field of benthic ecology. An
established regime of in-house QC checks will be adhered to in which a portion of each
technician's work is reviewed by a senior taxonomist; a failed check requires that all of that
technician's samples, since the last passed check, be re-sorted or re-identified (depending on
the assigned task). The same types of QC checks apply throughout the process of identifying
and quantifying the benthos; technicians and taxonomists have their work verified by a peer or
more senior taxonomist. The QC checks must be well documented in a laboratory notebook that
will be available to NCCA QA personnel upon request. The benthic data will be subject to an
audit of data quality during the 2-year period following the completion of the benthic community
assessments.

Evaluators: One  or more designated Contractor staff members who are qualified (i.e., have
participated in  lab audit discussions/training as  appropriate) in the  procedures of the NCCA
laboratory operations.

To Evaluate: Laboratories performing nutrient, sediment chemistry, sediment toxicity, whole fish
tissue processing and analysis, pathogen or subsampling, sorting, and taxonomic procedures to
analyze coastal samples.

Purpose: To identify and correct deficiencies during laboratory  operations and procedures.

    1.  Maria Smith and Joe Hall will review the  Laboratory and Assistance Visit Plan and
       Check  List for this lab process/indicator as appropriate with each Evaluator during lab
       audit conference calls.
    2.  Maria Smith and Joe Hall will send a copy of the final Plan and the final Check List
       pages,  NCCA lab manual and QAPP to  each participating Evaluator.
    3.  Schedule of lab visits will be made by the Evaluator in consultation with Maria Smith,  Joe
       Hall and the respective Laboratory Supervisor Staff.  Evaluators should be prepared to
       spend additional time in the laboratory if needed (see below).
    4.  Evaluators,  working with Maria Smith, will arrange the schedule of visitation with each
       participating Laboratory,.  Ideally,  each Laboratory will be evaluated within the first two
       weeks following initial receipt of samples, so that procedures can be corrected or
       additional training provided, if needed.
    5.  The Evaluator will view the performance of the laboratory procedures and QC Officer
       through one complete set of sample processing activities as detailed  on the Laboratory
       Evaluation and Assistance Check List.
          a.   Scheduling might necessitate starting the evaluation midway on the list of tasks
              for processing a sample, instead  of at the beginning. In that case,  the Evaluator
              will view the activities of the laboratory personnel when a new sample is started
              to complete the evaluation of the first activities on the list.
          b.   If laboratory personnel miss or incorrectly perform a procedure, the Evaluator will

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             note this on the checklist and immediately point this out so the mistake can be
             corrected on the spot. The role of the Evaluator is to provide additional training
             and guidance so that the procedures are being performed consistent with the
             Laboratory Methods manual, all data are recorded correctly, and paperwork is
             properly completed at the site.
   6.  When the sample has been completely processed or analyzed, the Evaluator will review
       the results of the evaluation with laboratory personnel and QC Officer, noting positive
       practices and problems (i.e., weaknesses [might affect data quality]; deficiencies [would
       adversely affect data quality]). The Evaluator will ensure that the laboratory personnel
       and QC Officer understand the findings and will be able to perform the procedures
       properly in the future.
a.      The Evaluator will record responses or concerns, if any, on the Laboratory Evaluation
and Assistance Check List.

b.  If the Evaluator's findings indicate that Laboratory staff are not performing the procedures
correctly, safely, or thoroughly, the Evaluator must continue working with these staff members
until  certain of their ability to process the sample properly so that data quality is not adversely
affected.

             i.   Maria Smith (202-566-1047)
             ii.   Joe Hall, EPA NCCA QA Officer (202-566-1241)
   7.  The QA official will contact the EPA  Project Leader (Gregory Colianni) or Alternate EPA
       Project Leader (Treda Grayson or John Macauley) to determine the appropriate course
       of action
   8.  Data records from samples previously processed by this  Laboratory will be checked to
       determine whether any samples must be redone.
   9.  Complete the Laboratory and Assistance Visit Plan and Check List for this lab
       process/indicator as appropriate, including a brief summary of findings, and ensure that
       all Team members have read this and signed off before leaving the Team.
   10. Make a copy of the Laboratory Evaluation and Assistance Check List.  Mail the original
       of each completed Laboratory Evaluation and Assistance Check List to Maria Smith :
       USEPA Headquarters, Ariel Rios Building, 1200 Pensylvania Ave, N.W., Washington,
       D.C. 20460.
Maria Smith and Joe Hall will review the returned Laboratory Evaluation and Assistance Check
Lists, note any issues, check off the completion  of the evaluation for each participating
Laboratory.  The original will be filed in the NCCA QA Officer file, Washington DC and pdf
versions will be emailed to the appropriate lab, state and regional contacts.

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                            7.      DATA ANALYSIS  PLAN
 The goal of the NCCA is to address two key questions about the quality of the Nation's
 coastal waters:

       •   What percent of the Nation's coastal waters are in good, fair, and poor condition for
          key indicators of chemical water quality, ecological condition, and suitability for
          recreation?
       •   What is the relative importance of key stressors (e.g., nutrients and pathogens) in
          impacting the biota?

The Data Analysis Plan describes the approach used to process the data generated during the
field survey to answer these two questions. Results from the analysis will be included in the final
report and used in future analysis.

7.1.    Data  Interpretation Background

The intent of data analyses is to describe the occurrence and distribution of selected indicators
throughout the estuaries and coastal waters of the United States within the context of regionally
relevant expectations. The analyses will culminate by categorize and reporting the condition of
coastal waters as  being good, fair, or poor condition. Statistical  analysis techniques appropriate
for using  data collected using probabilistic survey designs such as those described at EPA's
Aquatic Resource Monitoring website, http://www.epa.gov/nheerl/arm/index.htm, will serve as
the primary method for interpreting survey results. However, other data analyses will be used for
further assessment investigations as described below.

Because of the large-scale and multijurisdictional nature of this  effort, the key issues for data
interpretation are: the scale of assessment, selecting the effective  indicators across the range of
systems  included  in the survey, and determining thresholds for judging condition. An NCCA
Data Analysis work group will be created to address these points and to help strengthen NCCA
assessments.

         7.1.1.       Scale of Assessment

EPA selected the  sampling locations for the NCCA survey using a probability based  design,  and
developed rules for selection to meet certain distribution criteria, while ensuring that the design
yielded a set  of coastal areas that would provide for statistically valid conclusions about the
condition of the population of coastal areas across the nation.

         7.1.2.       Selecting Indicators

Indicators for the 2010 survey will basically remain the same as those used in the historic
National Coastal Report, with a few modifications. The most prominent change  in this year's
survey is the  inclusion of coasts along the Great Lakes. Therefore both sample  collection
methods  and laboratory methods reflect freshwater and saltwater matrices.

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The NCCA workgroup, based on recommendations from a state workshop held in 2008,
decided on a few modifications to the original NCCA indicators. The changes are:  1)
measuring Enterococcus levels as a human health indicator; 2) requiring the measurement of
photosynthetically active radiation (PAR) using instrumentation to help standardize the water
clarity indicator; 3) for sediment toxicity testing, lab methods will use Eohaustorius or
Leptochirus instead of Ampelisca sp. for saline sites and Hyalella for freshwater sites; 4)
ecological fish tissue studies will  be conducted using whole fish, and 5) fish community
structure, Total Suspended Solids (TSS), and PAHs in fish tissue will no longer be included.
7.2.    Datasets to be used for the Report
The Dataset used for the 2010 assessment consists of data collected during 2010 NCCA and
data from historic National Coastal Condition Reports (NCCRs) for tracking changes in water
quality data. Other data may be added as appropriate.

7.3.    Indicators  for the Coastal Assessment
        7.3.1.       Water Chemistry and Chlorophyll

A wide array of water chemistry parameters will be measured. Water chemistry analysis is
critical for interpreting the biological indicators. Chlorophyll-a, Secchi depth, light attenuation
and nutrient measurements will be used to create a water quality index and identify stressors.

        7.3.2.       Benthic Macroiinvertebrates

To distinguish degraded benthic habitats from undegraded  benthic habitats, EMAP and NCA
have developed regional (Southeast, Northeast, and Gulf coasts) benthic indices of
environmental condition (Engle et al., 1994; Weisberg et al., 1997;  Engle and Summers, 1999;
Van Dolah et al., 1999; Hale and Heltshe,  2008).

        7.3.3.       Sediment Chemistry/Characteristics

The NCCA  is collecting sediment samples, measuring the concentrations of chemical
constituents and percent TOC in the sediments, and evaluating sediment toxicity as described
in the QAPP, field operations manual and  laboratory operations manual. The results of these
evaluations will be used to identify the most-polluted the sediment quality index is based on
measurements of three component indicators of sediment condition: sediment toxicity, sediment
contaminants, and sediment TOC.  This information will also be used in identifying stressors to
ecological/biological condition.

        7.3.4.       Enterococci Data Analysis

The presence of certain levels of enterococci is associated  with pathogenic bacterial
contamination of the resource. A single  enterococci water sample will be collected at each site,

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then filtered, processed, and analyzed using qPCR. Bacterial occurrence and distribution will be
reported. Data interpretation will be enhanced by comparison to USEPA qPCR pilot studies as
well as to thresholds recommended from the Great Lakes qPCR studies. In addition, some
states are doing parallel studies with better known culturing techniques that have a vast
historical database which to compare.

        7.3.5.       Fish Chemistry

For the NCCA, both juvenile and adult target fish species will be collected from all monitoring
stations where fish were available, and whole-body contaminant burdens will be determined.
The target species typically included demersal (bottom dwelling) and pelagic (water column-
dwelling) species that are representative of each of the geographic regions. The EPA
recommended values for fish advisories will serve as the threshold against which to evaluate
risk.

7.4.    NCCR Index Development Approach
EPA intends to calculate the indices used in previous NCCR reports.  Information on this
approach, the indices and related thresholds can be found in the National Coastal Condition
Report III (EPA 2008.)

7.5.    Calculation of Population  Estimates

Once the individual indicator values are calculated for each sampling  location, population
estimates will be generated using the procedures outlined by EMAP and found on the Aquatic
Resource Monitoring website (give location). The population estimates will include estimates of
uncertainty for each indicator. The output of these analyses are the specific results that will
appear in the coastal assessment report.

7.6.    Relative Extent, Relative Risk and Attributable Risk Analysis

EPA intends to estimate the relative extent of poor conditions for each stressor, the relative risk
posed to biota by that stressor and the population attributable risk analysis as outline by Van
Sickle and Paulsen (2008).

7.7.    Other Change Analyses

Biological and stressor/chemical data from the NCCA and previous reports will be analyzed to
see what changes have occurred over time.

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 Table 7.1 Criteria for Assessing Dissolved Inorganic Nitrogen.
       Area
    Good
    Fair
     East/Gulf       <0.l mg/L     O.I-0.5 mg/L     >0.5 mg/L
     Coast sites
West Coast
sites
<0.5 mg/L
0.5- 1. 0 mg/L
>\ mg/L
     Hawaii,
     Puerto Rico,
     and Florida
     Bay sites
  <0.05 rng/L    0.05-0.1 mg/L   >0.l  mg/L
     Regional
     Scores
Less than 10%
of the coastal
  area was in
  poor condi-
tion, and more
  than 50% of
  the coastal
   area was
   in good
  condition.
 10% to 25%
of the coastal
 area was in
 poor condi-
tion, or more
 than 50% of
 the coastal
  area was
 in combined
poor and fair
  condition.
More than 25%
 of the coastal
   area was
    in  poor
   condition.
7.8.   Index Precision and Interpretation

NCCA indicators will be repeated at 10% of the sites during the summer 2010 index sampling
period. These repeat samples allow an assessment of the within-season repeatability of these
indicators and metrics. We will calculate the precision of a selection of site condition indicators
used in the NCCA. The basic measure of repeatability is RMSrep, the Root Mean Square of
repeat visits. The RMSrep is a measure of the absolute (unsealed) precision of the whole
measurement and analytical process, incorporating also short-term temporal variability within
the summer sampling period. One can envision RMSrep for a metric is an estimate of its
average standard deviation  if measured repeatedly at all sites, and standard deviations for each
site will be averaged across sites. For Log transformed variables, one can view the antilog of
the RMSrep as a proportional standard deviation. The antilog of 0.179 is 1.51. Then, for

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example the, RMSrep of 0.179 for Log10(PTL+1) means that the +/- error bound on a
measurement in at a site is the measured value times 1.51 and divided by 1.51. So, the +/-1
StdDev error bounds on a PTL measurement of 10 ug/L during the index period is (10 •*• 1.51) to
(10x1.51) or 6.6 to 15.1.
Another way of scaling the precision of metrics is to examine their components of variance. We
will calculate signal to noise rations for each indicator in determining whether they are
acceptable for use in the data analysis described above.  The ratio of variance among sites to
that due to measurement (or temporal) variation  within individual sites has been termed a
"Signal-to-noise" ratio. One can think of S/N as the ability of the metric to discern differences
among sites in this survey context. If the among-site variance in the region/large estuary/Great
Lake or nation is a meaningful variation in site condition, then the S/N is a measure of the ability
of a metric to discern site condition. This variance-partitioning approach is explained in
Kaufmann et al. (1999) and Faustini and Kaufmann (2007), where the authors referred to
RMSrep as RMSE and evaluated S/N in stream  physical habitat variables. In those publications,
the authors generally interpreted precision to be  high relative to regional variation if S/N >10,
low if S/N <2.0, and moderate if in-between. When S/N is over about 10, the effect of
measurement error on most interpretations is nearly insignificant within the national context;
between 6 and 10 these  effects are minor. Between S/N of 2 and 5, the effects of imprecision
should be  acknowledged, examined and evaluated. From 2 to 4 they are usually adequate to
make good-fair-poor classifications,  but there is some distortion of CDFs and a significant
limitation of the amount of variance that can be explained by approaches such  as multiple linear
regression (The magnitude of the within-site variance component limits on the amount of
among-site variance that can be explained by multiple linear regression using single visit data).
                                8.     REFERENCES
American Public Health Association. 2006. Standard Methods for the Examination of Water and
Wastewater. 21st Edition. American Public Health Association, Washington, D.C.

American Society for Testing and Materials. 1991. Guide for conducting 10-day static sediment
toxicity tests with marine and estuarine amphipods.  ASTM Standard Methods Volume 1104,
Method Number E-1367-90. American Society for Testing and Materials, Philadelphia, PA.

Arar, E.J., and J.B. Collins, 1992.  EPA Method 445.0: "In Vitro Determination of Chlorophyll
a and Pheophytin a in Marine and Freshwater Phytoplankton by Fluorescence" EPA/600/R-
2/121.

Barbour, M.T., J. Gerritsen, B.D. Snyder, and J.B. Stribling.  1999. Rapid Bioassessment
Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic Macroinvertebrates
and Fish, Second Edition. EPA 841-B-99-002. U.S. Environmental Protection Agency; Office of
Water; Washington,  D.C.

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CAS - Chemical Abstracts Service (CAS 1999)

Engle, V.D., J.K. Summers, and G.R. Gaston. 1994. A benthic index of environmental condition
of the Gulf of Mexico Estuaries.  Estuaries 17:372-384.

Engle, V.D., and J.K. Summers. 1999. Refinement, validation, and application of a benthic index
for northern Gulf of Mexico estuaries. Estuaries 22(3A):624-635.

Faustini, John M. and Philip R. Kaufman. 2007. Adequacy of visually classified particle count
statistics from regional stream habitat surveys. Journal of the American Water Resources
Association 43(5): 1293-1315. WED-06-126.

Federal Register, Part VIII, EPA. "Guidelines Establishing Test Procedures for the Analysis
of Pollutants Under the Clean Water Act: Final Rule and Proposed Rule."  40 CFR Part 136, Oct.
28,  1984.

FGDC, 1998. Content Standard for Digital Geospatial Metadata. FGDC-STD-001-1998, Federal
Geographic DataCommittee, Reston, VA-USA.

FGDC, 1999. Geospatial Metadata, Part 1:  Biological  Data Profile. FGDC-STD-001.1-1999,
Federal Geographic Data Committee, Reston, VA-USA.

Glaser, P.M.; Wheeler, G.A.; Gorham, E.; Wright, H.E., Jr. 1981. The patterned mires of the Red
Lake Peatland, northern Minnesota: vegetation, water chemistry, and landforms. Ecology. 69:
575-599.

Hale, S.S., and J.F. Heltshe. 2008. Signals  from the benthos:  Development and evaluationof a
benthic index for the nearshore Gulf of Maine. Ecological Indicators 8: 338-350.

Hawkins, C. P.,  R. H. Morris, J. N. Hogue, and J. W. Feminella. 2000. Development and
evaluation of predictive models for measuring the biological integrity of streams. Ecological
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Heinz Center. 2002. The State of the Nation's Ecosystems. The Cambridge University  Press.

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Quality Assurance Project Plan for                                               July 2010
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Quality Assurance Project Plan for                                              July 2010
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National Coastal Condition Assessment                                     Page 121 of 121

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