&EPA
EPA 820-R-13-001
Biological Assessment Program Review;
Assessing Level of Technical Rigor
to Support Water Quality Management
February 2013
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Front cover sources:
1. EPA; 2. USGS; 3. USGS; 4. EPA
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SEPA
United States Office of Science and Technology February 2013
Environmental Protection Washington, DC 20460 EPA820-R-13-001
Agency
Biological Assessment Program Review:
Assessing Level of Technical Rigor to Support
Water Quality Management
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The Biological Assessment Program Review February 2013
Disclaimer
The discussion in this document is intended to provide information on advancements in the
field of biological assessments and on use of biological assessments to support state water
quality management programs. The statutory provisions and the U.S. Environmental Protection
Agency (EPA) regulations described in this document contain legally binding requirements. This
document is not a regulation itself, nor does it change or substitute for those provisions or
regulations. The document does not substitute for the Clean Water Act (CWA) or EPA or state
regulations. Thus, it does not impose legally binding requirements on EPA, states, tribes, or the
regulatory community. This document does not confer legal rights or impose legal obligations
on any member of the public.
While EPA has made every effort to ensure the accuracy of the discussion in this document, the
obligations of the regulated community are determined by statutes, regulations, and other
legally binding requirements. In the event of a conflict between the discussion in this document
and any statute or regulation, this document will not be controlling.
The general descriptions provided here might not apply to a situation depending on the
circumstances. Interested parties are free to raise questions and objections about the
substance of this document and the appropriateness of the application of the information
presented to a situation. This document does not make any judgment regarding any specific
data gathered or determinations made by a state or tribal biological assessment program or the
use of such data in the context of implementing CWA programs. Mention of any trade names,
products, or services is not and should not be interpreted as conveying official EPA approval,
endorsement, or recommendation.
This is a living document and might be revised periodically. EPA could revise this document
without public notice to reflect changes in EPA policy, guidance, and advancements in field of
biological assessments. EPA welcomes public input on this document at any time. Send
comments to Susan Jackson, Office of Science and Technology, Office of Water,
U.S. Environmental Protection Agency, 1200 Pennsylvania Avenue, Mail Code 4304T,
Washington, DC 20460.
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The Biological Assessment Program Review February 2013
BIOLOGICAL ASSESSMENT PROGRAM REVIEW:
ASSESSING LEVEL OF TECHNICAL RIGOR TO SUPPORT
WATER QUALITY MANAGEMENT
Contact Information
For more information, questions, or comments about this document, please contact Susan Jackson,
U.S. Environmental Protection Agency, at Office of Science and Technology, Office of Water,
U.S. Environmental Protection Agency, 1200 Pennsylvania Avenue, Mail Code 4304T, Washington, DC
20460, or by email at jackson.susank@epa.gov.
Acknowledgments
Thank you to the following state and tribal agencies for their support with developing and piloting the
biological assessment program review process:
Alabama Department of Environmental Management
Arizona Department of Environmental Quality
California State Water Resources Control Board
Connecticut Department of Environmental Protection
Colorado Department of Public Health and Environmental Management
Florida Department of Environmental Protection
Fort Peck Tribes (Assiniboine and Sioux)
Illinois Environmental Protection Agency
Indiana Department of Environmental Management
Iowa Department of Natural Resources
Maine Department of Environmental Protection
Massachusetts Department of Environmental Protection
Michigan Department of Environmental Quality
Minnesota Pollution Control Agency
Missouri Department of Natural Resources
Montana Department of Environmental Quality
New Hampshire Department of Environmental Services
New Mexico Environment Department
Ohio Environmental Protection Agency
Rhode Island Department of Environmental Management
Texas Commission on Environmental Quality
Vermont Department of Environmental Conservation
Wisconsin Department of Natural Resources
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The Biological Assessment Program Review February 2013
Acknowledgments (cont.)
Thank you to the following scientists for their support and, for several, their leadership in developing
the biological assessment program review process:
Chris Yoder, Midwest Biodiversity Institute
Susan Davies, Maine Department of Environmental Protection
Lester Yuan, Janice Alers-Garcia, Thomas Gardner, EPA Office of Science and Technology
Susan Holdsworth, Sarah Lehmann, Ellen Tarquinio, Treda Grayson,
EPA Office of Wetlands, Oceans, and Watersheds
Wayne Davis, Office of Environmental Information
Stephen Silva, Katrina Kipp, Jennie Bridge,
Hilary Snook, Diane Switzer, EPA Region 1
Linda Hoist, Edward Hammer, EPA Region 5
Charlie Howell, Michael Schaub, EPA Region 6
Gary Welker, Catherine Wooster-Brown, EPA Region 7
Tina Laidlaw, EPA Region 8
Terrance Fleming, EPA Region 9
David Peck, Steve Paulsen, John Stoddard, James Lazorchak, Scot Hagerthey,
Carolina Penalva-Arana, Giancarlo Cicchetti,
EPA Office of Research and Development
Charles Hawkins, Bernard Sweeney, Society of
Freshwater Science Taxonomic Certification Committee
Michael Barbour, Jeroen Gerritsen, Clair Meehan, Christoph Quasney,
Jennifer Stamp, James Stribling, Tetra Tech, Inc.
IV
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The Biological Assessment Program Review February 2013
Contents
Chapter 1: Biological Assessment Program Evaluation 1
1.1 Background 1
1.2 Why Is the Level of Technical Rigor Important? 1
1.3 The Technical Foundation for a Biological Assessment Program 3
1.4 The Biological Program Review Process 4
1.5 Benefits of a Rigorous Biological Assessment Program 6
1.5.1 Implications for Technical Program Development 9
1.5.2 Benefits of a Biological Assessment Program Review 10
Chapter 2: The Technical Elements of a Biological Assessment Program 11
2.1 The Technical Elements 12
2.1.1 Index Period: Characterizing and Accounting for Temporal Variability (Element 1) 12
2.1.2 Spatial Sampling Design (Element 2) 15
2.1.3 Natural Variability: Characterizing and Accounting for Spatial Variability (Element 3) 19
2.1.4 Reference Site Selection (Element 4) 22
2.1.5 Reference Conditions (Element 5) 24
2.1.6 Taxa and Taxonomic Resolution (Element 6) 27
2.1.7 Sample Collection (Element 7) 31
2.1.8 Sample Processing (Element 8) 33
2.1.9 Data Management (Element 9) 35
2.1.10 Ecological Attributes (Element 10) 37
2.1.11 Discriminatory Capacity (Element 11) 41
2.1.12 Stressor Association (Element 12) 43
2.1.13 Professional Review (Element 13) 46
2.2 Determining the Overall Technical Program Level of Rigor 47
Chapter 3: The Program Evaluation Process 51
3.1 Introduction to the Evaluation Process 51
3.2 Preparation for the Review 53
3.2.1 Identifying Participants 53
3.2.2 Materials Provided as Basis for Program Review 54
3.2.3 Preparation of Documents 55
3.3 Part 1: Overview of Current Water Quality Program 56
3.3.1 Introduction and Overviews 56
3.3.2 Monitoring and Assessment 57
3.3.3 Reporting and Listing (CWA sections 305[b] and 303[d]) and TMDLs 58
3.3.4 Water Quality Standards 59
3.3.5 Integration of Monitoring, Reporting, Standards, and Management 60
3.3.6 Self-Assessments 61
3.4 Part 2: Technical Elements Evaluation 61
3.4.1 Technical Elements of State Biological Assessment Programs: A Process to Evaluate
Program Rigor and Comparability 61
3.4.2 Technical Elements Checklist 62
3.5 Preparation of Technical Memorandum 62
3.6 Action Plan Development 62
3.7 Summary 64
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References Cited 66
Acronyms and Abbreviations 80
Glossary 82
Appendix A: Agenda for On-Site Interaction Meeting 89
Appendix B: Interview Topics for Agency Review 92
Appendix C: Self-Assessments by State/Tribal Agency Managers 100
Appendix D: Technical Memorandum Template 128
Appendix E. Technical Elements Checklist 133
Figures
Figure 1-l.The critical technical elements 3
Figure 1-2. Examples of typical upgrade activities state or tribal water quality agencies have taken
to incrementally strengthen their technical programs. The example characteristics
provided in column three are relevant to a biological assessment program's technical
capability to distinguish incremental biological change along a gradient of increasing
stress. Improved ability to discriminate biological changes supports more detailed
description of designated aquatic life uses and derivation of biological criteria 5
Figure 2-1. Geometric Watershed Design used to support multiple management needs in the Big
Darby Creek watershed, Ohio (Ohio EPA 2004) 17
Figure 2-2. New York has integrated a probabilistic spatial survey design (A) into its routine
rotating integrated basin studies program (B) (Source: NYSDEC 2009) 18
Figure 2-3. Example of bioregions as established for the Mississippi River 21
Figure 2-4. Example approach for assessing representativeness of reference sites. The solid line
shows the cumulative distribution function of watershed areas for different streams
in the assessed population, and the open circles show the watershed areas of the
available reference sites. In this example, presence of reference sites for a watershed
area is given by the density of the open circles. The majority of the watershed areas
are well-represented by reference sites, because there is a high density of open
circles above steep portions of the solid line; except for the largest streams (> 1,000
km2). (USEPA2006) 25
Figure 2-5. Standard deviations of 25th percentile fish assemblage Index of Biotic Integrity (IBI)
scores estimated by randomly drawing reference sites at a given sample size (x-axis)
five times for wading sites in the Lake Huron/Lake Erie Plain (HELP) and Erie Ontario
Lake Plain (EOLP) ecoregions of Ohio (modified from Yoder and Rankin 1995a) 26
Figure 2-6. Stream sampling methods 32
Figure 3-1. Flow chart of the 3-day biological assessment program evaluation process 52
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Tables
Table 1-1. Example discussion questions and topics on use of biological assessments to support
water quality management program information needs 7
Table 2-1. Definitions of the technical elements 11
Table 2-2. Examples of biological assessment index periods for different state water quality
agencies 14
Table 2-3. Biological and other ecological attributes used to characterize the BCG 39
Table 2-4. Scoring associated with technical element levels of rigor 48
Table 2-5. Allowable deviation of technical elements scores for each of the four levels of rigor 49
Table 2-6. State Pilot Biological Assessment Reviews: Correspondence of the level of rigor to
adoption or development of refined aquatic life uses and/or biological criteria in
state WQS 50
VII
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The Biological Assessment Program Review February 2013
Foreword
State and tribal water quality agencies face challenges to ensure that the best available science
serves as the backbone of their monitoring and assessment programs. The degree of
confidence with which biological assessment information can be used to answer water quality
management questions relies to a considerable degree on a program's level of technical rigor.
This document provides a process, including materials, for states and tribes to evaluate the
technical rigor and breadth of capabilities of a biological assessment program. The review is
intended to help states and tribes answer the following questions:
What are the strengths of my technical program?
What are the limitations of my technical program?
How do I determine priorities and allocate resources to further develop the technical
capabilities of my existing program?
If I want to use biological assessments to more precisely define my designated aquatic
life uses and develop numeric biological criteria, how do I begin technical development?
Using the program review process described in this document, states and tribes can identify the
technical capabilities and the limitations of their biological assessment programs and develop a
plan to build on the program strengths and address the limitations. The U.S. Environmental
Protection Agency (EPA) recommends that the review include both EPA regional participants
and agency program managers and staff, and that it be facilitated by a technical expert with
expertise in biological assessments and biological criteria derivation. As part of the review
process, a state or tribe evaluates how it currently uses biological assessment information to
support its overall water quality management program and considers potential future
applications using information gained by a strengthened technical program.
The document includes a description of 13 technical elements of a biological assessment
program, provides a checklist for evaluating the level of technical development for each
element, and includes a method for characterizing the overall level of program rigor. As a
technical program is improved, biological assessment information can be used with increasing
confidence to support multiple water quality program needs for information. Such needs
include more precisely defined aquatic life uses and approaches for deriving biological criteria,
monitoring biological condition, supporting causal analysis, and developing stressor-response
relationships.
This document is intended to be used as a "how to" manual to guide technical development of
a biological assessment program for providing information to meet multiple water quality
information needs. Water quality agencies can use the outcomes of the programmatic review
to develop the technical strengths of their biological assessment programs and allocate
resources to build as robust programs as their resources will allow. The highest level of
technical development as described in this document can be thought of as a well-equipped
toolbox. Not all tools need to be applied all the time and in all situations. For a water quality
VIII
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program, the type and level of quality of a biological assessment tool (e.g., a collection method,
monitoring design, or analytical approach) will depend on the question being asked and the
specific environmental circumstances. For this reason this document does not, and is not
intended to, establish minimum expectations regarding the amounts or types of biological data
that might be considered necessary in the context of decision making in Clean Water Act
regulatory programs. However, understanding the different programmatic expectations for the
biological assessment data guides the technical review and recommendations for technical
development.
IX
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CHAPTER 1: BIOLOGICAL ASSESSMENT PROGRAM EVALUATION
1.1 Background
A biological assessment is an evaluation of
the biological condition of a water body
using surveys of the structure and function
of resident biota, including migratory biota
that reside in the water body for at least
one part of their life cycle (USEPA 2011b).
Biological assessment information is
important to effectively and accurately
answer water quality management
questions about condition, protection, and
restoration. It is a principal monitoring tool
for state and tribal water quality agencies
(referred to throughout as water quality agencies) and is used to varying degrees and purposes by
all 50 states and increasingly by tribes (USEPA 2002b, 2011c). Over the past 20 years, water
quality agencies have developed different abilities to use biological assessment information for
water quality management. An agency's ability to use this information at the appropriate level of
precision and accuracy to answer a given management question is called its technical capability.
The technical capability of a program is dependent on its level of technical rigor. For the purposes
of this document, a technically rigorous biological assessment program:
Uses scientifically accepted and documented methods.
Adheres to methods and protocols.
Documents quality assurance and quality control.
Provides information to support multiple WQM programs.
1.2 Why Is the Level of Technical Rigor Important?
The technical rigor of a biological assessment program
determines the degree of accuracy and precision in
assessing biological condition and deriving stressor-
response relationships. With increasing technical rigor,
a water quality agency gains increased confidence in
data analysis and interpretation, as well as more
comprehensive support for a variety of water quality
management activities, including the following:
More precisely defining goals for aquatic life use
protection.
Deriving biological criteria.
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The Biological Assessment Program Review
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Identifying high quality waters and establishing biological condition baselines.
Identifying waters that fail to support designated aquatic life uses.
Supporting development of water quality criteria.
Conducting causal analysis.
Monitoring biological response to management actions.
This document is intended to be used as a road
map for technical development of a biological
assessment program. It provides a step-by-step
process for evaluating both the technical rigor of a
water quality agency's biological assessment
program and the extent to which the water quality
agency uses the information to support overall
water quality management. The evaluation is based
on the degree of technical development of the
biological assessment program's survey design,
methods, analysis, and interpretation; how
biological assessments are integrated into and supported by the monitoring program; how the
agency currently uses biological assessments to support its water quality programs; and how it
intends to use biological assessments in the future.
The end goal of this evaluation
process is an action plan for
technical program development
and recommendations to enhance
the use of biological assessments
to support the agency's overall
water quality management
program (USEPA 2011c). The plan
specifies incremental steps for
technical and program
development based on the
strengths and gaps identified in
the evaluation.
To date, this process has been
applied to biological assessment
programs for river and streams and reviews conducted with 22 states and 1 tribe (Yoder and
Barbour 2009). However, the technical elements and the review process are applicable to other
water body types with water body-specific modifications for biological assessment design,
methods, and data analysis.
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1.3 The Technical Foundation for a Biological Assessment Program
Technical Elements of a
Biological Assessment Program
Biological assessment design
1. Index period
2. Spatial sampling design
3. Natural variability
4. Reference site selection
5. Reference conditions
Data collection and compilation
G.Taxa andtaxonomic resolution
7. Sample collection
8. Sample processing
9. Data management
Analysis and interpretation
10. Ecological attributes
11. Discriminatory capacity
12. Stressor association
13. Professional review
Figure 1-l.The critical technical elements.
The determination of a biological assessment
program's level of technical rigor is on the basis of
evaluating 13 technical elements that provide the
foundation of its biological assessment design, data
collection and compilation, and analysis and
interpretation (Figure 1-1). Biological assessment
design includes temporal and spatial considerations in
developing a monitoring program and selection of
sampling sites, characterizing and accounting for
natural variability, and determining reference
condition. Data collection and compilation includes
field and laboratory protocols and data handling,
typically included in agency standard operating
procedures (SOPs). Analysis and interpretation
comprise all of the data analysis, interpretation, and
review procedures used after data are obtained. The
13 technical elements are based on U.S.
Environmental Protection Agency's (EPA's)
Consolidated Assessment and Listing Methodology
(CALM) guidance on collection and use of water
quality data and information for environmental decision making (USEPA 2002a), and on EPA's
Evaluation Guidelines for Ecological Indicators (Jackson et al. 2000; Kurtz et al. 2001). The
evaluation guidelines described 15 guidelines in 4 areas (termed "phases" in the Guidelines)
comprising conceptual relevance of the indicator, feasibility of implementation, response
variability, and interpretation and utility. The CALM guidance describes seven critical technical
elements of a biological assessment program. In that guidance EPA also describes four levels of
technical program rigor, Levels 1 through 4, with Level 4 being the highest level of rigor. As
described in chapter 2 of this document, the original 7 critical technical elements have been
refined and expanded to 13 elements on the basis of a water quality agency's assessment
program reviews conducted beginning in 2004 (Yoder and Barbour 2009; USEPA 2010b).
The technical elements and the level of development for a rigorous biological assessment
program are discussed in more detail in chapter 2. Assessment of the technical elements is the
technical backbone of the program review process, and it provides the detailed information
needed by an agency program to develop its technical program. An estimate of overall level of
program rigor is assigned based on the scoring of the technical elements that correspond with a
program's increasing ability to detect incremental levels of biological change along a gradient of
stress, associate biological response to stressors and their sources, and integrate biological
assessments with other environmental data and information.
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The Biological Assessment Program Review February 2013
1.4 The Biological Program Review Process
The biological program review is a systematic process to evaluate the technical rigor of a water
quality agency's biological assessment program and to identify logical next steps for overall
program improvement. The review is typically conducted over two to three days for both a
thorough evaluation of the technical elements and for agency cross-program discussions on the
use of biological assessment data and information to support the overall water quality
management program. The purpose of the cross-program discussions is to provide an
opportunity for managers and staff from different water quality programs to identify the type
and level of rigor of biological assessment that best addresses their information needs.
Additionally, personnel can share their needs and timing for information to optimize collection
and delivery of the data. These discussions might reveal areas for program improvement and
coordination that will foster more efficient and comprehensive application of biological
assessments. An improved understanding of how an agency uses biological assessment
information in its water quality programs helps answer the "so what" question for why an
agency would allocate staff and resources for technical development.
The review includes both EPA regional participants and agency program managers and staff,
and it is typically facilitated by an independent technical expert with expertise in biological
assessments and in biological criteria derivation.
The review team first evaluates the 13 technical elements of a biological assessment program.
Each technical element receives a score on the basis of its current state of technical
development. These scores are then summed for an overall program scorea higher score
reflecting a higher level of technical development, corresponding with increased capability and
confidence in use of biological assessment data.1 A Level 4 assignment is the highest ranking,
and Level 1 is the lowest ranking. These levels reflect sequential stages in technical
development of a biological assessment program and are intended as a guide for assessing
progress and targeting resources.
The review process is designed to evaluate the key gaps in a technical program and to identify
incremental steps for addressing the gaps. The scoring of the individual elements provides the
essential information for identifying these technical gaps. Incremental improvements in the
individual technical elements are followed, often in a short time, by corresponding
improvements in the technical capability of the overall program (Figure 1-2). At all levels of
technical development described in this document, a state or tribal program is able to use
biological assessment information to carry out Clean Water Act (CWA) activities. For example, a
defensible decision that aquatic life use is impaired can be based on a qualitative visual
observation of overwhelming biological evidence such as nearly total dominance of pollutant
1 Because the overall score is the result of the summation of individual scores for the 13 separate elements, the
overall score does not establish minimum expectations regarding a state's ability to make decisions in context of
different CWA regulatory programs. At all levels of technical development, biological assessment information can
be used to support water quality decisions.
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LEVEL OF
TECHNICAL
PROGRAM RIGOR
Level 1
EXAMPLE
UPGRADE ACTIVITIES
Program maintenance and
refinements as needed
(e.g., aquatic life use refinement
based on new monitoring data
and information; develop method
to measure third assemblage)
Develop method to measure
second assemblage; Paired
monitoring for biological
response and stressor measures
Upgrade data analysis methods;
Improve taxonomic identification
for one assemblage to highest
practical taxonomic resolution,
(e.g., genus or species level)
Select sample collection,
processing methods, index period,
and analysis measures
EXAMPLE
CHARACTERISTIC OF
TECHNICAL PROGRAM
Finer increments of
biological change along a
continuous stress gradient.
The number of increments
that can be distinguished is
dependent upon waterbody
type and natural climatic
and geographic factors
Three levels of biological
change along a continuous
gradient of stress
Two levels of biological
change along a continuous
gradient of stress
Biological assessments
detect extremes (e.g., best
existing and severely
impacted). Large degree of
uncertainty in assessing
changes between extremes
No
Program
Establish biomonitoring using
critical technical elements
None
Figure 1-2. Examples of typical upgrade activities state or tribal water quality agencies have taken to
incrementally strengthen their technical programs. The example characteristics provided in column three are
relevant to a biological assessment program's technical capability to distinguish incremental biological change
along a gradient of increasing stress. Improved ability to discriminate biological changes supports more detailed
description of designated aquatic life uses and derivation of biological criteria.
tolerant organisms (e.g., scuds, worms, snails), a pervasive algae bloom, or a fish kill. As the
technical program is improved, the agency will be able to use biological assessment information
with increasing confidence to more precisely define aquatic life uses, develop biological criteria,
and, in conjunction with whole effluent, physical, chemical, and land use data, identify stressors
and their sources.
Matching the existing level of technical rigor with the intended use of the information can
provide insight on the benefit of technical development. An agency can use this understanding
to guide decisions and priorities on technical development of its biological assessment program.
As part of the review, agency managers and staff from the biological assessment program and
other water quality programs discuss how biological assessment information is currently used
to support the overall water quality management program and on program enhancements that
might lead to more comprehensive and effective use of biological assessment information. On
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The Biological Assessment Program Review February 2013
the basis of the reviews conducted beginning in 2004 (Yoder and Barbour 2009; USEPA 2010b),
an agency's ability to comprehensively and effectively use biological assessment information is
supported by:
Refined aquatic life use classification to protect existing conditions and maintain
improvements.
Numeric biological criteria adopted into water quality standards (WQS).
Coordinated biological, whole effluent toxicity (WET), chemical, and physical monitoring
to support both condition assessments and causal analysis.
Program managers and staff from the monitoring and assessment programs, WQS, CWA section
305(b) report, 303(d) list, Total Maximum Daily Load (TMDL), National Pollutant Discharge
Elimination System (NPDES), and nonpoint source programs jointly discuss information needs
and program schedules. A water quality agency might support development of a rigorous
technical biological assessment program, but if the types and quality of data, data collection,
and analysis are not aligned with water quality management program information needs and
implementation schedules, the information might not be most effectively used. The cross-
program discussion will help reveal any gaps and inconsistencies that the agency can then
address. The long-term goal is to develop a well-integrated biological assessment program that
produces information with the appropriate degree of accuracy, precision, and confidence to
support multiple water quality program information needs (Table 1-1). The results of these
discussions do not affect the scoring of the technical elements but can inform an agency's
decision on level of technical development to best support its management objectives and
program priorities.
Following the review, the independent technical expert prepares a technical memorandum that
describes the program's current level of rigor for the 13 technical elements and identifies the
technical gaps revealed in the evaluation. In conjunction with the agency review participants,
the technical expert develops recommendations to improve specific technical elements. This
information helps the agency target resources more efficiently, address weaknesses, and
incrementally strengthen its program to better support water quality management decisions.
More information about the biological assessment review process is in chapter 3.
1.5 Benefits of a Rigorous Biological Assessment Program
As stated previously, at all levels of technical development, biological assessment information
can be used to support water quality decisions. However, the degree of confidence in the use of
information will increase with technical development. For example, improvements in the ability
to detect changes in biological assemblages along a gradient of stress can enhance precision in
describing high-quality waters and setting incremental restoration targets, as well as
discriminating between intermediate levels of condition (e.g., Diamond et al. 2012).
Characteristics of high level programs include improved sensitivity in the biological indices to
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Table 1-1. Example discussion questions and topics on use of biological assessments to support
water quality management program information needs.
Self Assessment Question
Program Implementation
Does the biological assessment program produce
adequate data and information to develop biological
criteria, provide detailed descriptions of designated
aquatic life uses, support identification and
protection of high-quality waters, and inform use
attainability analysis (UAA)?
Narrative descriptions of aquatic life use classes and
attendant numeric biological criteria incorporate
elements of natural classification strata consistent with
underlying distinction of aquatic ecotypes at appropriate
spatial scale for application of the information. The
biological assessment program provides data and
information to define biological expectations for a
specific water body or watershed and support water
quality management decisions to protect existing
conditions and support improvements.
How is the biological monitoring and assessment
program conducted to support multiple water quality
management program objectives? Does the program
work with other water quality management
programs to coordinate biological (including WET),
chemical, and physical monitoring and assessments?
Monitoring and assessment is integrated into the overall
management of surface water quality to support both
determination of general condition and causal analysis.
Spatial design is sufficient to detect and characterize
chemical and non-chemical pollution gradients and to
associate measured changes in biotic assemblages with
specific or categories of stressors. Results are expressed
to support multiple program uses including WQS
attainment, CWA sections 305(b) reporting and 303(d)
listing, CWA section 402 NPDES program, and watershed,
reach, and site-specific support (i.e., investigations,
watershed planning, site-specific water quality criteria
development, UAA).
Is there a method developed for stressor
identification and implemented as part of the water
quality program? How is the information used to
support multiple water quality management
programs?
Empirical relationships between biological measures and
chemical/physical parameters are well-developed and
documented. Information is used to support
statewide/regional development and refinement of water
quality criteria and support stressor identification as an
integral part of the assessment process. This, in turn,
supports development of TMDLs.
measure incremental biological changes along a gradient of stress (Levels 3 and 4) and a more
complete assessment of the community by measuring two or more assemblages (Level 4). A
Level 4 program should also be able to support more expedient and robust causal analysis,
because the biological assessments are coordinated with WET, chemical, and physical
monitoring. Field data are linked with information on sources of stress and watershed
characteristics to support source identification. Two examples of program benefits shown by
states that have piloted the biological assessment review follow.
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The Biological Assessment Program Review February 2013
Example 1: Aquatic life use refinement. A biological assessment program with a high level of technical rigor
provides for a greater degree of confidence in an agency's ability to establish biological thresholds that protect
existing conditions, determine potential for improvements, and monitor to track progress and maintain
improvements. For example, based on measured changes in biotic assemblages, Vermont has the technical
capability to discriminate multiple increments of biological change along a gradient of stress that spans excellent to
severely impacted conditions. Based on these data and information, Vermont has adopted three aquatic life use
classes in its WQS (e.g., excellent, very good, good). The state has set aquatic life uses classes for its streams and
rivers to maintain existing high-quality conditions. The specific use class assigned to a water body is based on its
current condition, and, if degraded, its potential for improvement. Ohio has likewise adopted multiple levels of
aquatic life use classes (e.g., exceptional warmwater and warmwater habitat). Additionally, Ohio has established
biological expectations for agricultural drainage ditches and permanently altered streams (e.g., modified warm
water habitat and limited resource waters, respectively) following a use attainability analysis (UAA) process. Ohio's
use assignments undergo periodic review and upgrades based on routine, coordinated chemical, physical, and
biological monitoring and assessments, including data from WET monitoring.
For both states, biological assessments conducted in conjunction with physical, whole effluent, and chemical
monitoring enables them to evaluate the potential for improved conditions in their streams and rivers and
consequently set appropriate and attainable goals in their WQS (e.g., designated aquatic life uses). Additionally,
routine monitoring provides new data that is used to upgrade waters to a higher aquatic life use class as conditions
improve (USEPA2011c).
Example 2: Causal analysis. A finding of biological impairment does not assist management in correcting the
problem unless causes of the impairment can be identified. A common use of stressor identification, or causal
analysis, is in the TMDL program in situations for which a water body has been determined to have one or more
impaired designated uses but the pollutants causing or contributing to the use impairments are not identified at
the time. A monitoring program that collects comprehensive biological (including WET), physical, and chemical
information in a coordinated manner will have the ability to examine evidence for causes of observed impairments
and to develop stressor-response relationships that can inform stressor identification (e.g., Yoder and Rankin
1995b; Suter et al. 2002). For example, the Maine Department of Environmental Protection (MDEP) evaluated the
condition of the Pleasant River watershed with biological indices for benthic macroinvertebrates and algae in
combination with chemical and physical data and information. Located in southern Maine, the Pleasant River
watershed is primarily forested with some agriculture and increasing amounts of residential development in the
downstream portions of the watershed. The Pleasant River has a water quality goal of Class Bgood quality
conditions.
MDEP sampled algal and macroinvertebrate communities in several locations on the Pleasant River. Biological
assessment results showed that the headwater reach attained Class B. Further downstream, the
macroinvertebrate samples attained Class B. However, some of the downstream algal samples attained a lower
level of quality comparable to Class C conditions (i.e., waters in fair condition). The river segment was also listed as
impaired because it did not attain the Class B dissolved oxygen criterion. MDEP used water chemistry data, habitat
evaluations, and diagnostic algal and macroinvertebrate metrics to determine that phosphorus enrichment was
the probable stressor for these downstream sites. To prepare for developing a TMDL, MDEP evaluated the
watershed and identified some farms and residential areas as potential sources of nutrients in the lower part of
the watershed. The combination of biological assessments for multiple taxonomic groups and associated chemical,
habitat, and land use information allowed MDEP to complete a thorough and more expedient evaluation of the
Pleasant River watershed. As a result, MDEP has started developing a TMDL that will effectively target
management actions needed to maintain biological conditions in the headwaters and to restore downstream
portions of the watershed.
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Use of multiple biological assemblages and coordinated biological, WET, chemical, and physical
monitoring are characteristics of a Level 4 biological assessment program, and these capabilities
can lead to improved confidence in estimating stress-response relationships. A relational
database that enables data export and analysis via query supports this function. This level of
technical development improves an agency's efficiency in identifying water quality limited
waters that must be placed on a state or tribe's CWA section 303(d) list, conducting causal
analysis, and assigning probable cause, or causes, of impairment. As a result, an agency should
be able to more efficiently develop the appropriate management action to address a TMDL (or
suitable alternative means of achieving WQS) when a pollutant has been identified as the cause
of a biological impairment. A well-established, well-supported, and comprehensive monitoring
program then provides the data needed to track progress and evaluate the effectiveness of the
management actions taken, whether monitoring discharges and tracking the effects of permit
limits or monitoring the implementation of best management practices (BMPs) for nonpoint
source pollution. Paired stressor-response data might also be used to develop or refine
chemical water quality criteria (Cormier et al. 2008; USEPA 2010c), and it has been used to
identify benchmarks for conductivity (USEPA 2011a).
Overall, a monitoring program that integrates biological assessment, WET, chemical, and
physical data is key for the most effective implementation of the biological assessment program
and supports use of biological assessments to more precisely define aquatic life uses and derive
numeric biological criteria. Additionally, when the monitoring schedule coincides with the cycle
of WQS establishment and review, CWA section 305(b) reporting and section 303(d) listing,
TMDL development, NPDES permitting, and nonpoint source program implementation,
biological and other environmental data are available when needed by water quality
management programs. Several states have improved cross program coordination through a
rotating basin approach.
A well-established biological monitoring and assessment program will further benefit an
agency's water quality program if comparable or consistent sample collection methods and
data analysis protocols are developed in conjunction with the biological monitoring programs of
other agencies (e.g., at local level and adjacent states, tribes; federal). This approach will
support development of regionally consistent taxonomy for biological data and will help
address data gaps regarding regionally appropriate, taxon-specific tolerance values and other
ecological traits. Such consistent data allow for shared use of reference site data across
jurisdictional boundaries. In some places there is a paucity or total lack of reference sites
comparable to minimally disturbed conditions. The ability to share data and expand reference
site network beyond jurisdictional boundaries might support establishing more robust
reference conditions.
1.5.1 Implications for Technical Program Development
The technical capabilities of Level 1 and 2 programs are appropriate for some, but not all, water
quality program uses. For example, a Level 1 program can typically differentiate water bodies in
the very best and worst conditions, whereas a Level 2 program can more confidentially assess
good and poor conditions. Both these programs can make defensible determinations of failure
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to fully support a water body's designated aquatic life use, but they might fail to detect initial
and significant changes in biological condition caused by anthropogenic stress. Some degraded
water bodies might not be accurately assessed, and, therefore, no actions are initiated to
remediate and restore them. Southerland et al. (2006) estimated that up to 25 percent of
impaired sites would escape detection (i.e., would pass as unimpaired, or false negatives)
simply from lax reference site-selection criteria. This situation is of particular concern if a
threshold is selected at the low boundary of a reference condition.
1.5.2 Benefits of a Biological Assessment Program Review
An agency can use the biological program review to determine the capabilities of its biological
assessment program in a consistent, systematic manner that supports further technical
development and enables midcourse review and refinement. The review will help determine if
information is collected and analyzed with the accuracy and precision appropriate to address a
variety of water quality management issues. The agency will be able to propose refinements to
its water quality program to enable more comprehensive and efficient use of biological
assessment information to support water quality management in a variety of water quality
programs (e.g., NPDES permitting, TMDLs). This process and its outcomes help communicate
the value of further technical development to agency management and to the public. The
process, steps, and workshop materials for the biological program review are further discussed
in chapters 2 and 3 of this document.
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CHAPTER 2: THE TECHNICAL ELEMENTS OF A BIOLOGICAL
ASSESSMENT PROGRAM
A biological assessment program's level of rigor is dependent on the quality and level of
resolution of 13 technical elements (Table 2-1).
Table 2-1. Definitions of the technical elements
Biological Assessment Design
Data Collection and Compilation
Ana lysis and
Interpretation
Technical Element
Index Period
Spatial Sampling
Design
Natural Variability
Reference Site
Selection
Reference
Conditions
Taxa and Taxonomic
Resolution
Sample Collection
Sample Processing
Data Management
Ecological Attributes
Discriminatory
Capacity
Stressor Association
Professional Review
Definition
A consistent time frame for sampling the assemblage to characterize and
account for temporal variability.
Representativeness of the spatial array of sampling sites to support statistically
valid inference of information over larger areas (e.g., watersheds, river and
stream segments, geographic region) and for supporting water quality standards
(WQS) and multiple programs.
Characterizing and accounting for variation in biological assemblages in response
to natural factors.
Abiotic factors to select sites that are least impacted, or ideally, minimally
affected by anthropogenic stressors.
Characterization of benchmark conditions among reference sites, to which test
sites are compared.
Type and number of assemblages assessed and resolution (e.g., family, genus, or
species) to which organisms are identified.
Protocols used to collect representative samples in a water body including
procedures used to collect and preserve the samples (e.g., equipment, effort).
Methods used to identify and count the organisms collected from a water body,
including the specific protocols used to identify organisms and subsample, the
training of personnel who count and identify the organisms, and the methods
used to perform quality assurance/quality control (QA/QC) checks of the data.
Systems used by a monitoring program to store, access, and analyze collected
data.
Measurable attributes of a biological community representative of biological
integrity and that provide the basis for developing biological indices.
Capability of the biological indices to distinguish different increments, or levels,
of biological condition along a gradient of increasing stress.
Relationship between measures of stressors, sources, and biological assemblage
response sufficient to support causal analysis and to develop quantitative stress-
response relationships.
Level to which agency data, methods, and procedures are reviewed by others.
The following section describes each technical element and provides a template for assigning a
level of technical rigor to each element. Section 2.2 describes how these scores are summarized
to estimate an overall level of technical rigor for a biological assessment program.
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2.1 The Technical Elements
2.1.1 Index Period: Characterizing and Accounting for Temporal Variability
(Element 1)
(Lowest) 1.0
2.0
3.0
4.0 (Highest)
Temporal variability is
not taken into account.
Sampling period
established based on
practices of other
agencies and/or
literature. Sampling
outside the index is not
adjusted for temporal
influence.
Index period established
based on a priori
assumptions regarding
temporal variability of
biological community.
Effects of the use of index
period are documented.
Data collected outside the
index period data might be
adjusted to correct for
temporal influences.
Temporal variability is
fully characterized and
taken into account for all
data. Agency information
needs and index periods
are coordinated so that
adherence to an index
period is strict.
Biological communities vary over time due to the life cycles of the targeted organisms
(e.g., reproduction, recruitment, growth, emergence, and migration) and temporal variations in
environmental conditions (e.g., changes in flow), so the characteristics of a biological sample
can also vary depending on when that sample is collected. This temporal variability must be
taken into account when interpreting biological data and assessing biological condition. Two
approaches are commonly used: index periods and continuous models.
An index period is a contiguous time period used to minimize variation among biotic samples
associated with systematic phonological changes in population densities and assemblage
structure (Munne and Prat 2011; Kosnicki and Sites 2011). Selection of an index period can be
based on a priori, existing knowledge regarding the predictable temporal changes in
assemblage structure described above, when resident populations are comparatively stable
(e.g., periods of growth between recruitment and emergence), and when potential exposure to
anthropogenic stressors is highest (e.g., Resh and Rosenberg 1984,1989; McElravy et al. 1989;
Barbour et al. 1996; Bailey et al. 2004; Bollmohr and Schultz 2009). The index period can be
further refined or based on analysis of data collected throughout the year to identify those
periods in which assemblage composition is most stable. When selecting an index period, a
biological assessment program also typically considers availability of sampling crew and
accessibility to and safety of sampling sites.
Continuous models can also be used to characterize and account for natural temporal
variations in the characteristics of biological assemblage. These statistical models estimate
relationships between different biological attributes and the season or day of the year when
the samples were collected (e.g., Hawkins 2006). For example, day of the year was the single
most important predictor in development of an observed/expected (0/E) index in North
Carolina, and the 0/E model was adjusted for phonological shifts in species abundance
(Hawkins 2006). The day of the year was the single most important predictor in development of
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the 0/E index and the model adjusted for phonological shifts in species abundance. Continuous
models can be applied to data collected in index periods or across multiple seasons. Indeed,
approaches that combine data collected during index periods with models to account for
temporal variations within index periods are often the most effective means of accounting for
temporal variations. Also, one can calibrate multiple seasonal indicators and indexes, or
develop an average or composite annual characterization based on multiple samples (e.g.,
Furse et al. 1984; Linke et al. 1999; Cao and Hawkins 2011; Pond et al. 2012).
Scoring of the index period element depends on how thoroughly a program has considered and
documented the effects of different index periods on the characteristics of biological data and
on decisions derived from this biological data. Example evaluation questions are:
Is sampling carried out primarily within a defined index period?
- If not, are the program's indices structured to account for temporal variability?
What are the justifications for the defined index period, and has variability within the
index period been quantified?
If an alternative approach has been selected, does this approach adequately account for
temporal variability?
Are the monitoring and other water quality management programs coordinated their
schedules so that data are provided when the programs need it? Does lack of
coordination result in monitoring outside of the index period?
Programs that score highly on this element have documented the effects of the index period or
an alternative approach to address temporal variability. Additionally, the monitoring and other
water quality management programs have coordinated their schedules so that program
information needs (e.g., condition assessments, permit reviews, total maximum daily load
[TMDL] development) are coordinated with data delivery.
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Frequently Asked Question
Question: What is the optimal time of year to select as an index period?
Answer: Selection of an index period is part of the overall design process that takes into account scientific
knowledge, objectives, costs, logistics, and information desired from the monitoring program (Hughes and Peck
2008). For example, seasonal phenology influences the species composition in streams; late-instar (and hence easy
to identify) stoneflies and mayflies occur in early spring, but in early summer they might be present only as very
small early instars (e.g., McCord and Lambrecht 2006). Fish sampling is generally avoided in the spawning seasons
of anadromous fish (Hughes and Peck 2008). Safety and logistics are also issues, as is scheduling the sequence of
field, laboratory, data processing, and reporting tasks; sampling might be dangerous during the spring freshet
(snowmelt), and high elevation streams might only be accessible in the summer (Hughes and Peck 2008). As
depicted in Table 2-2, the index period can vary by state and assemblage group.
Table 2-2. Examples of biological assessment index periods for different state water quality
agencies
Winter
Dec
Jan
Feb
Spring
Mar
Apr
May
Summer
Jun
Jul
Aug
Fall
Sep
Oct
Nov
Vermont
(Benthos)
Vermont (Fish)
New Jersey
_
Maryland
(Benthos)
Maryland (Fish)
Mississippi
_
New Mexico
Iowa (Benthos)
Iowa (Fish)
Arizona
Idaho
Benthos
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2.1.2 Spatial Sampling Design (Element 2)
(Lowest) 1.0
2.0
3.0
4.0 (Highest)
Study design
consisting of isolated,
single, fixed-point
sites.
Low density fixed station
design. Multiple sites are
used for assessment of a
water body or watershed
condition. Spatial coverage
suitable for general
condition assessments.
Non-random designs at
coarse scale used (e.g., 4-8
digit hydrologic unit code
[HUC]). Inference of site
data to larger unit of
assessment based on "rules
of thumb" and might be
supplemented by
upstream/downstream
assessments.
Low density random or
stratified random
sampling design which
allows for a statistically
valid inference of
biological condition to
a spatial unit larger
than a site. The primary
goal is to assess
aggregate condition
and trends on a
statewide or regional
basis.
High density (e.g., intensive)
monitoring at comprehensive
spatial sampling design
suitable for watershed
assessments (e.g., 10-12 digit
HUC) and in support of
multiple water quality
management program needs
for information (e.g.,
condition assessments, use
refinement, use attainability
analyses [UAAs], permits). As
needed, the spatial sampling
combines monitoring designs
to optimize cost and
efficiency in data collection
and analysis (e.g.,
combination of upstream-
downstream, intensive,
probabilistic, and/or pollution
gradient designs). Typically
includes a rotating sequence
of watershed units organized
to provide data for
management program
support.
Water quality programs have multiple needs for information (e.g., status and trends, stressor
identification, targeted studies, discharge monitoring). This technical element addresses how
well a biological assessment program is able to (1) deploy monitoring designs that address the
suite of water quality program information needs; (2) cover the pollution gradients that are
relevant to the impairments that are detected; and (3) provide data relevant to the scale
required for specific management program needs (e.g., stream segment, watershed, region,
statewide) and that support statistically valid inferences of site data to the unit of assessment.
Study design pertains to the spatial array of sampling sites to support assessments at
watershed and stream- or river-segment specific scales. It also includes the ability to provide
biological assessment data and information to address multiple water quality program
questions (e.g., status and trends, environmental outcomes of management actions, as well as
relevant targeted studies such as discharge monitoring and TMDL implementation) at the same
scale at which management is being applied. A biological assessment program will need to
determine what sampling design, or combination of sampling designs, will provide the full suite
of information needed to address its priority management questions (e.g., for site-specific use
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attainability determinations, biological criteria derivation, targeted assessments, causal
analysis, statewide and regional status).
Whether single or multiple sampling designs are employed, they will need to support multiple
management program support tasks. Multiple, overlapping monitoring designs can be
appropriately scaled to address these specific needs when the designs are incorporated into an
overall spatial network for monitoring (e.g., upstream-downstream; intensive, probabilistic,
gradient design). For example, sampling upstream and downstream of a discharge is conducted
to specifically quantify the effects of that discharge. A gradient design is appropriate for
refinement or development of biological or other types of water quality criteria. Spatially
intensive sampling can be designed for specific studies and purposes including site-specific
criteria development or refinement. A probabilistic monitoring design can be tailored for
condition assessments at different spatial scales (e.g., watershed, basin, ecological region,
statewide). In some cases, with upfront planning, the monitoring designs can be
complementary with sampling sites providing data relevant to more than one purpose.
Study designs also need to factor in adjustments for effects of natural gradients. This
adjustment is typically accomplished iteratively when accounting for natural spatial variability
(see technical element three) and dependent upon assessment objective (e.g., define stressor
gradient, assess condition, determine cause of impairment in a stream segment). For example,
in streams and rivers, the structure of aquatic assemblages changes naturally and predictably as
one moves downstream from steeper, narrow, shaded, small steams to low-gradient, open-
canopied, large streams (Vannote et al. 1980). Sampling sites might be located in linear
juxtaposition to one another in a river or stream network. In these situations observations at
nearby sites might be spatially autocorrelated and, hence, not statistically independent of one
another (e.g., NAS 2002). These considerations should be addressed in the spatial sampling
design and in subsequent analysis of data to accurately and precisely define the expected
biological community for a water body (e.g., refined aquatic life use) and to minimize risk of
making nonattainment decisions on the basis of natural changes in assemblage as one samples
further downstream.
Scoring of this technical element is based on the degree to which the selected sampling sites
can inform multiple water quality information needs and support decisions at different spatial
scales. Example evaluation questions are:
Is the spatial study design sufficient to represent the majority of water types in the area
of interest?
Are all pollution impacts and gradients adequately characterized?
For condition assessments, how well can inferences be made to unsampled sites within
the unit of assessment (e.g., site, stream segment, watershed, basin, statewide,
ecological region)?
For specific water bodies of concern, can valid inferences be made on differences in
condition upstream and downstream of a discharge, and on changes before and after
implementation of best management practices (BMPs)?
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Programs that achieve high scores on this technical element have implemented an integrated
sampling design, or combination of sampling designs, that provide the data and information
necessary to support water quality management decisions at multiple spatial scales (e.g.,
specific sites, entire watersheds, basins, ecological regions, statewide).
Frequently Asked Questions
Question: What type of study design can efficiently support statewide condition assessments and 305(b) reports?
Answer: A probabilistic sampling design can be used to randomly select sampling sites from the population of
water bodies so that inferences from this random subsample can be made to the entire population (Herlihy et al.
2000; Olsen and Peck 2008). A probabilistic design is the most efficient sampling design for statewide condition
assessments such as the Clean Water Act (CWA) section 305(b) reports since all potential sampling locations have a
known probability of being selected and inference to larger geographical area is statistically robust (e.g., Thompson
1992; Olsen et al. 1999; Olsen et al. 2009). When resources are not available to sample all basins statewide in any
particular year, a rotating basin approach can be implemented.
Index of Biotic Integrity (IBI)
Big Darby Creek System
1990s
Average IBI
(Scale ofO to 60, with 60
indicating the highest quality)
1990-2001
Mussel Species Richness
(Live or Fresh Dead Only)
1990 - 2002
0 species
l-especles
7-12 species
13 -18 species
19 -24 species
25 -30 species
Question: What type of
study design can support
assessing use
designations, conducting
use attainability analyses
(UAAs), and providing
information about
multiple stressors at a
watershed scale?
Answer: There are
several sampling designs
that could be used when
appropriately designed to
answer these questions,
including a survey,
gradient, or random
designs tailored to the
appropriate spatial scale.
For example, a geometric
and intensive watershed
design was used at the 11-digit hydrologic unit code (HUC) scale in Big Darby Creek, Ohio, and, when considering
serial autocorrelation between adjacent sites, is nearly equivalent to a census of the stream reaches of the
watershed (Figure 2-1). The data were used to determine if the current aquatic life use of stream and river
segments was appropriate and attainable and then to determine the status of each site. The data were also used
to delineate impairments for reporting (e.g., CWA section 305[b]/303[d]), and causes and sources were
determined to support specific water quality management actions (i.e., TMDLs, National Pollutant Discharge
Elimination System [NPDES] permits, stormwater permitting, 401 certifications) and support watershed planning
(i.e., section 319 planning and implementation). Ohio conducts four to five of these assessments annually with a
rotating basin approach, and, in the aggregate, each contributes to a statewide inventory of streams and rivers and
Figure 2-1. Geometric Watershed Design used to support multiple management
needs in the Big Darby Creek watershed, Ohio (Ohio EPA 2004).
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is part of a database that supports many program maintenance and developmental needs. These data are
aggregated upwards to produce regional and statewide assessments for meeting CWA 305b reporting and internal
program goal tracking (e.g., the Ohio 2020 goals).
Question: What are the benefits of combining probabilistic design surveys with intensive surveys designed to
answer multiple water quality management questions?
Answer: Developing the technical capacity to conduct different types of survey designs enhances the breadth and
depth of the monitoring program's ability to answer multiple water quality management questions and to more
efficiently leverage resources. For example, in 2008, New York State Department of Environmental Conservation's
(NYSDEC's) Stream Biomonitoring Unit merged a random probabilistic design survey with its legacy statewide basin
studies. This hybrid survey design allows it to fit the needs of two primary objectives of its program: surveying
targeted of-interest sites, and creating an unbiased random data set (Figure 2-2). Targeted sites include those that
allow for the characterization of regional reference conditions, long-term temporal trend monitoring, assessment
of unassessed waters, and the monitoring of sites that are of department, regional, and/or public interest. The
random data set gives the ability to project aquatic life use attainment in an un-biased, statistically sound manner
across the entire state, and provides uniform comparability between basin data sets and other national data sets.
Targeted sites make up approximately 60 percent of the total number of sites sampled each year while random
sites compose 40 percent.
r, i.
'- 'V1" "i -
/**::.':'. :
..; » :-y .:*:.<.
. >k. . ; .."
Figure 2-2. New York has integrated a probabilistic spatial survey design (A) into its routine rotating integrated
basin studies program (B) (Source: NYSDEC 2009).
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2.1.3 Natural Variability: Characterizing and Accounting for Spatial Variability
(Element 3)
(Lowest) 1.0
2.0
3.0
4.0 (Highest)
No or minimal
partitioning of natural
variability in aquatic
ecosystems. Does not
incorporate
differences in
watershed
characteristics such as
size, gradient,
temperature,
elevation, etc.
Classification scheme is
based on assumed, first-
order classes. These
include strata such as
fishery-based cold or
warmwater classes.
There is no formal
consideration of
regional strata such as
bioregions or
aggregated ecoregions.
Intra-regional strata
such as watershed size,
gradient, elevation,
temperature are not
addressed. Usually
applied uniformly on a
statewide basis.
A fully partitioned and
stratified classification
scheme or modeling
approach is employed.
Classes and/or continuous
models are defined to take
critical details of spatial
variability into account.
Inter-regional landscape
features and phenomena
are appropriately
sequenced with intra-
regional strata.
Subcategories of lotic
ecotypes are defined (e.g.,
includes the full strata of
lotic water body types).
Characterization of spatial
variability is confined
within jurisdictional
boundaries.
Scheme to fully account for
natural variation is
periodically refined and
updated as new data and
methods become available.
Classes, continuous models,
or both, are examined to
identify the most
appropriate scheme for
monitoring and
assessment, regulatory
support, and cost-
effectiveness. Developed at
scales that transcend
jurisdictional boundaries
when necessary to
strengthen inter-regional
classification outcomes;
recognizes the full
zoogeographical aspects of
biological assemblages.
Biological assemblage structure varies spatially among different sites, often associated with
variations in abiotic environmental conditions (Theinemann 1954; Hynes 1970; Poff 1997). Both
local (e.g., water temperature, flow, and alkalinity) and regional environmental conditions (e.g.,
basin topography, climate) strongly influence assemblage structure, and when interpreting
biological data and assessing condition, natural variations in assemblage structure must be
characterized and taken into account to ensure that changes in assemblage structure can be
confidently attributed to anthropogenic rather than natural factors.
Well-developed schemes to account for natural variation use a combination of large-scale
physical characteristics (e.g., watershed drainage size, elevation, geographic location) and local
site characteristics (e.g., temperature, alkalinity, substrate) (Moss et al. 1987; Reynoldson et al.
1997; Bailey et al. 1998; Marchant et al. 1999; Joy and Death 2002; Hawkins et al. 2000a;
Oberdorff et al. 2002). The principal approaches used are classification (or typology),
continuous models, and combinations of discrete and continuous models.
Classification schemes define classes of water bodies such that sites in each class are assumed
to be similar with one another in terms of naturally varying abiotic factors. Then, biological
assemblages observed at sites in each class are examined to determine if they are more similar
to one another than among classes. These classes can be defined a priori based on an ecological
understanding of natural factors that structure biological assemblages (Omernik 1987; Rabeni
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and Doisy 2011) to help design sampling strategies that represent all water body types in a
study area. Classification schemes can also include classes of water bodies that pertain to
inherent environmental requirements (e.g., warm and cold water, strata), differences in
discrete lotic strata (headwaters to large rivers), and continuous changes in assemblage
structure across natural environmental gradients (e.g., Moss et al. 1987). Classes can also be
specified a posteriori by statistically examining how assemblage structure varies across
different environmental gradients and defining discrete classes based on the results of these
analyses (Gerritsen et al. 2000). In either case, the biological condition at a particular site is
assessed by comparing to reference conditions in the class to which the site belongs.
Natural variations in assemblage structure can also be taken into account using models that
represent changes in structure over continuous environmental gradients (Crowns 2009;
Hawkins and Vinson 2011; van Sickle and Hughes 2000). These models are based on statistical
analyses that can be used to infer changes in assemblage structure due to different
environmental variables (Clarke et al. 1996; Bailey et al. 1998; Marchant et al. 1999; Hawkins et
al. 2000b; Simpson and Norris 2000; Joy and Death 2002). When a model is used to assess a
site, a site-specific prediction of biological characteristics is calculated, and the observed
characteristics assessed relative to this prediction. This information can also be used to
supplement or refine discrete classification approaches.
A comprehensive classification and/or modeling scheme is dependent on the spatial density of
the monitoring program. Sufficient spatial coverage is needed to test or verify a proposed
classification and/or modeling scheme (see Technical Element 2).
Scoring of Technical Element 3 is based on the degree to which the scheme accounts for
observed natural variability in biological assemblage structure. Example evaluation questions
are:
Does classification or modeling the effects of natural gradients sufficiently reduce
natural variability relative to anthropogenic variability?
Does the classification scheme and/or modeling process sufficiently include all the
common regional and watershed strata in the study area?
Is the approach sufficient to support the precision and accuracy needed in estimates of
biological index values?
Does the classification and/or model take into account information and considerations
from beyond a state or tribe's jurisdictional boundaries?
Programs that score highly in this technical element have demonstrated that their scheme to
describe natural variability (whether classification and/or continuous models) accounts for the
major sources of natural variability in the study area, and that the majority of the remaining
variability in biological characteristics can be attributed to human activities.
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Frequently Asked Questions
Question: What is meant by an ecoregional
classification for biological assessment?
Answer: Partitioning the water bodies of an
agency by natural variability in the biota results in
a classification that can improve assessment of
ecological condition. As an example, natural
classification in Mississippi resulted in
five bioregions (not counting the delta region in
gray) as a basis for biological assessment (Figure
2-3). Bioregions are geographically distinct regions
of water bodies that roughly correspond to
ecoregions or aggregations of ecoregions.
Question: How would a multivariate cluster
analysis serve as a form of classification?
Answer: Clustering the biological data from
reference sites reveals the inherent natural
variability among of sites. Clusters can be
selected that represent classes for assessment
membership.
Figure 2-3. Example of bioregions as established for
the Mississippi.
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2.1.4 Reference Site Selection (Element 4)
(Lowest) 1.0
2.0
3.0
4.0 (Highest)
Informal best
professional judgment
(BPJ) used in selection
of control sites. No
screens are used.
Limited, if any,
documentation and
supporting rationale.
Based on "best
biology" (i.e., BPJ on
what the best biology
is in the best water
body). Minimal non-
biological data used.
Minimal
documentation.
Selection based on
narrative descriptions of
non-biological
characteristics. Combines
BPJ with narrative
description of land use
and site characteristics.
Might use chemical and
physical data thresholds
as primary filters.
Based on quantitative
descriptions of non-biological
characteristics with primary
reliance on abiotic data on
landscape conditions and land
use. Chemical and physical data
might be used as secondary
filters or in a hybrid approach
for severely altered landscapes.
Independent data set used for
validation.
Reference site selection is the basis for developing benchmarks against which a biological
monitoring program can assess the biological condition of test sites (e.g., Hughes et al. 1986;
Barbour et al. 1996; Bailey et al. 2004; Stoddard et al. 2006; Hawkins et al. 2010). Reference site
selection is primarily based on abiotic factors that define sites that are "least stressed," or
ideally, "minimally stressed" by anthropogenic stressors and include knowledge of whether
invasive species are present (e.g., Hughes et al. 1986; Karr and Chu 1999; Bailey et al. 2004).
Abiotic characteristics and attributes should be the principal screens for selecting candidate
reference sites because such screens avoid circularity that is inherent in including ambient
biological characteristics to define reference sites for assessing biological condition.
Factors to be considered in selecting reference sites include human population density and
distribution, proximity to the influence of discharges, proximity to physical modifications of
stream and river channels, road density, and the proportion of mining, logging, agriculture,
urbanization, grazing, or other land uses. Candidate reference sites are evaluated with respect
to these factors to determine the degree of human modification that has occurred. Sites that
are minimally disturbed by potential stressor(s) are considered to be in reference condition
(Bailey et al. 2004; Stoddard et al. 2006). Ideally, sites are eliminated if they have undergone
direct human modification, especially to riparian zones and instream habitat (Bryce et al. 1999).
However, in some pervasively altered regions or altered systems, "least disturbed" sites that
represent the best available conditions have been used (e.g., Angradi et al. 2009).
Examples of evaluation questions are:
Do factors for reference site selection emphasize abiotic measures of anthropogenic
activity?
Are procedures for selection of sites well documented? Do those procedures include
consideration of watershed development, near stream development, and riparian
condition?
Are chemical, physical, and whole effluent toxicity (WET) sampling data used to validate
either the absence of anthropogenic disturbance or the level of allowed disturbance?
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The Biological Assessment Program Review February 2013
Programs that score highly in this technical element use several layers of abiotic filters to
identify reference sites for their study area, primarily based on landscape data from the
surrounding catchment and other information that characterizes the level of disturbance.
Independent data sets are used to validate reference site selection.
Frequently Asked Questions
Question: How do factors for reference site selection influence calibration of a biological index or indicator and
setting a threshold for biological criteria or for CWA section 303(d) listing decisions?
Answer: Biological criteria are typically derived from a reference site database (USEPA 1990,1998, 2001). The
reference site approach is typically also a basis for biological listing methodologies and for U.S. Environmental
Protection Agency's (EPA's) national surveys of stream condition (Herlihy et al. 2008). The factors for reference site
selection help define the quality of the reference condition (e.g., undisturbed, minimally or moderately disturbed,
least disturbed) (Stoddard et al. 2006). Herlihy et al. (2008) examined the effects of different quality of reference
sites from the large database of the U.S. Wadeable Streams Assessment (WSA). Poorer quality reference sites
(equivalent to relaxing the factors for reference site selection to accept more sites) resulted in assessments in
which more test sites were similar to reference than assessments done with reference sites selected based on
more stringent site selection factors. In other words, when the reference sites are influenced by human
disturbance, an agency might lose its ability to accurately define the desired biological condition and to
differentiate biologically degraded sites from reference. The quality of the reference sites as defined by the factors
for reference site selection can inform selection of a biological threshold. The percentile selection should be based
on the degree to which human activities influence the study area. For example, in the WSA, the threshold for a
specific ecological region was adjusted from 10 to 25 percent of the reference site distribution to account for the
presence of pervasive human disturbance at reference sites (Herlihy et al. 2008).
Question: What if the pool of reference sites has to include sites with substantial disturbance even though the
sites are least-disturbed in the context of the region? For example, in the Midwest, row crops and grain farming
are the primary land use, and virtually no unaffected water bodies exist.
Answer: Regions with extensively altered landscapes might require a model to extrapolate current conditions to a
reasonable reference. For example, a PCA-based regression model was used to project "true" reference in regions
where all reference sites are highly altered (Herlihy et al. 2008). Kilgour and Stanfield (2006) developed regressions
between biotic condition and percent impervious cover, and extrapolated biotic condition for very low impervious
cover scenarios. In a slightly different approach when naturally occurring conditions can be estimated, Chessman
and Royal (2004) used species responses to temperature, flow regime, and riverbed composition to predict the
species composition of different rivers with given combinations of naturally occurring temperature, flow, and bed
composition. In some cases, an agency might manage to the least disturbed condition and set incremental
restoration targets that support improvements as technology and BMPs are applied. If appropriate, the
expectations for an adjacent ecological region could be used to establish reference. For example, Ohio concluded
that least affected reference sites did not exist in the Lake Huron/Lake Erie Plain (HELP) ecological region and used
the biological expectations for a neighboring ecological region to determine a biological threshold. The key step is
to recognize when minimally altered conditions do not exist, and then derive a reasonable alternative for deriving
a protective biological criteria.
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2.1.5 Reference Conditions (Element 5)
(Lowest) 1.0
2.0
3.0
4.0 (Highest)
No reference
condition has been
developed. Biological
data are assessed
using BPJ or based on
the presence of
targeted or iconic
taxa.
Reference condition
based on biology of an
estimated 'best' site or
water body. Single
reference sites are used
to assess biological data
collected throughout a
watershed. A site-
specific control or
paired watershed
approach might be
used.
Reference condition is
based on a regional
aggregate of reference
site information. Data
representing most of
the major natural
environmental gradients
but limited in number
and/or spatial density.
Overall number and
coverage of reference
sites insufficient to
support statistical
evaluation of the
biological condition at
test sites.
Reference condition is based
on data from many reference
sites that span a\[ major
natural environmental
gradients in the study area.
Reference condition can be
estimated for individual sites
by modeling biota-
environmental relationships.
The number of reference sites
is sufficient to support
statistical evaluation of
biological condition at test
sites. Reference sites are
resampled periodically. In
highly altered regions or water
body types, alternative
methods are used to develop
reference condition.
A primary goal for a biological assessment program is to estimate the expected biological
condition (reference condition) for individual sites as accurately and precisely as possible. The
reference condition serves as the benchmark for judging condition of the site and as basis for
derivation of biological criteria. This technical element considers the number of reference sites
that are available and the degree to which those reference sites account for natural
environmental gradients (e.g., elevation, water body size) (Figure 2-4). This element also
considers whether the number of reference sites is sufficient to support appropriate use
designation and the derivation of numeric biological criteria. It is important to consider how
well the reference site network is re-monitored and reevaluated. Reference condition should
also be tracked by the periodic resampling of reference sites and as an integral function of the
overall monitoring program.
Using a representative network of reference sites ensures that the assessment of a test site is
based on a comparison with its most appropriate benchmark. Accordingly, development of
meaningful reference conditionsalso requires an adequate spatial coverage to obtain a
sufficient sample of reference sites.When sufficient reference site data are not available,
assessments might not be possible or might be conducted with more uncertainty. In regions
where all water bodies are severely altered, alternative methods might be used, including
historical data, models, or hindcasting (e.g., Dodds and Oakes 2004; Kilgour and Stanfield 2006;
Angradietal. 2009).
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The Biological Assessment Program Review
February 2013
Scoring of this technical element is based on the degree to which a sufficient number, or
network, of reference sites are available to establish reference condition. Example evaluation
questions are:
Is the pool of reference sites sufficient to characterize the natural gradients in the study
area (e.g., basin, ecological region, statewide)?
Is the number of reference sites sufficient to support the use designation and derivation
of biological criteria?
Are reference sites systematically resampled to track changes in reference condition
overtime?
In regions or water bodies with no adequate reference sites, are alternative methods
used effectively (e.g., historical data, modeling)?
High level programs should demonstrate that the network of reference sites fully represents all
the major natural environmental gradients in the study area and that the number of reference
sites is sufficient to support both appropriate use designation and derivation of attendant
biological criteria. Figure 2-4 provides an example approach for assessing the
representativeness of reference sites.
&
E
^
O
p
o
0.1 1 10 100 1000
Watershed area
Figure 2-4. Example approach for assessing representativeness of reference sites. The solid line shows the
cumulative distribution function of watershed areas for different streams in the assessed population, and the
open circles show the watershed areas of the available reference sites. In this example, presence of reference
sites for a watershed area is given by the density of the open circles. The majority of the watershed areas are
well-represented by reference sites, because there is a high density of open circles above steep portions of the
solid line; except for the largest streams (> 1,000 km2). (USEPA 2006)
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The Biological Assessment Program Review
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Frequently Asked Questions
Question: How does the number of reference sites (N) affect characterization of biological characteristics at a
regional scale?
Answer: The number of reference sites affects both the ability to account for spatial variability (see Technical
Element 3) and the precision with which thresholds can be specified. As discussed in Technical Element 3, many
natural abiotic environmental factors can influence assemblage structure, and the number of reference sites
directly affects the number of these factors that can be taken into account. For example, macroinvertebrate
assemblage structure might vary primarily with changes in stream size (or catchment area) and, secondarily, with
changes in alkalinity. Linear regression models generally require at least 10 sites per explanatory variable to
accurately estimate a relationship, so at least 20 reference sites are required to model changes in assemblage
structure with respect to both stream size and alkalinity. Additional reference sites that span other natural
gradients would provide increased capabilities to more precisely specify natural expectations for different types of
streams in the study area.
Once spatial variability is taken into account, distribution of expected index values derived from reference sites
must be quantified so that index values at test sites can be evaluated. More specifically, to assess condition, one
must test whether index values at a test site are within the range of index values observed in reference sites.
Increased numbers of reference sites allows one to more precisely estimate the reference distribution, and
therefore, more confidently assess test sites.
Question: How does the number of reference sites (N) affect the derivation of numerical biological criteria?
Answer: Determining the appropriate number of reference sites for deriving biological criteria is usually most
applicable on a regional basis because of differences in reference site heterogeneity both within and between
regions. In a more heterogeneous region, where natural conditions are more variable among streams, either (1) a
larger reference sites pool will be necessary to accurately derive a biological criteria threshold, or (2) further
partitioning of the natural variability through classification analysis might be needed. As illustrated in Figure 2-5,
the variability in reference quality is reduced as the number of reference sites increases to estimate the biological
criteria threshold.
o
^ 5
LO 4
CM
° 3
>
CD
0 2
^
CO 1
0
i i
n n
~
\ n
\
o XN n
Q NN n
x^ H IsT fv D F
dT^ w >x VCP
^o'-Qfi^SSsa
pj ^QU |_|
1 | | | | 1
v_J L!y
Ecoregion
o HELP
n EOLP
1 10 100
Sample Size
Figure 2-5. Standard deviations of 25th percentile fish assemblage Index of Biotic Integrity (IBI) scores estimated
by randomly drawing reference sites at a given sample size (x-axis) five times for wading sites in the Lake
Huron/Lake Erie Plain (HELP) and Erie Ontario Lake Plain (EOLP) ecoregions of Ohio (modified from Yoder and
Rankin 1995a).
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The Biological Assessment Program Review
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2.1.6 Taxa and Taxonomic Resolution (Element 6)
(Lowest) 1.0
2.0
3.0
4.0 (Highest)
One taxonomic
assemblage (e.g.,
benthic
macroinvertebrates,
fish, algae, aquatic
macrophytes). Very
coarse taxonomic
resolution (e.g.,
order/family).
Expertise: amateur
naturalist or stream
watcher. Validation:
none. QA/QC: none.
One taxonomic
assemblage. Low
taxonomic resolution
(e.g., family). Expertise:
novice or apprentice
biologist. Validation:
family level certification
for macroinvertebrates.
No certification
available for fish or
algae. QA/QC: mostly
for taxonomic
confirmation of voucher
collections. Some
sorting QA/QC
implemented.
One taxonomic assemblage. Fine
taxonomic resolution:
genus/species for benthic
macroinvertebrates and algae,
species for fish. Expertise: trained
taxonomist. Validation: genus-
level certification or equivalent
for benthic macroinvertebrates.
Expert fish taxonomist or
equivalent. Formal courses or
training in algal taxonomy.
QA/QC: addresses measuring bias,
precision, and accuracy in all
phases of sample processing
through identification (e.g.,
outside validation of
identification); voucher collection
maintained.
Same as Level 3
except that two or
more taxonomic
assemblages are
assessed. Rationale
for selection of
taxonomic groups
should be well
documented.
This taxonomic resolution technical element addresses the resolution to which organisms are
taxonomically identified (order, family, genus, or species) and, for the highest level programs,
how many different assemblages are included. Four assemblages have been primarily used in
freshwater biological assessment and in making aquatic life use attainment decisions: benthic
macroinvertebrates, fish, algae, and aquatic macrophytes. Methods for measuring amphibian
assemblages (e.g., early life stages of salamanders) are also being developed (Moyle and Randall
1998; Whittier et al. 2007a, 2007b) for certain water body types such as primary headwater
streams (Ohio EPA 2012). Each assemblage has different habitat ranges and preferences and
might be susceptible to anthropogenic stressors in different manners and degrees.
As more assemblages are assessed, one can more confidently infer the condition of the entire
biological community (e.g., Carlisle et al. 2008). Hence, collecting and assessing different
assemblages provides a more complete assessment of the condition of aquatic life in a water
body. For example, assemblages that represent more than one trophic level (primary
producers, consumers, predators) might increase the ability to both assess the overall condition
of the aquatic community and measure responses to multiple stressors that might affect the
community. Additionally, some detectable changes in assemblages, or members of an
assemblage, might provide a measure of initial stress and provide information helpful to
protection of high-quality waters (e.g., Petty et al. 2010; Brooks et al. 2011; Danielson et al.
2012).
Collected organisms must be identified taxonomically before one can infer biological condition
from a sample of these organisms, and the resolution of these identifications (e.g., order,
family, genus, species) can influence inferences regarding the degree of biological alteration
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The Biological Assessment Program Review February 2013
(e.g., Lenat and Resh 2001; Waite et al. 2004; Feio et al. 2006; Hawkins 2006; Pond et al. 2008;
Cao and Hawkins 2011). In some cases, a finer level of taxonomic resolution allows one to
better assess the sensitivity of the collected organisms to different types of stress. For example,
the temperature requirements of mayflies in a certain family might vary substantially, so
identifying taxa to genus or species when possible within this family might allow one to better
understand the impacts of altered temperature on a water body (Vannote and Sweeney 1980).
Conversely, in some regions, the number of different genera in each family might be
comparatively low, so identification to family yields nearly as much information as identification
to species or genus (Hawkins and Norris 2000b). In other regions, taxonomic resolution can be
limited by existing taxonomic information on native fauna (e.g., Buss and Vitorino 2010).
Taxonomic identification requires substantial training and practice, and quality
assurance/quality control (QA/QC) of the identifications is critical for maintaining consistent
standards of identification (e.g., Stribling et al. 2008).
Scoring of this technical element is based primarily on the resolution of the taxonomic
identifications and on the level of QC and the number of assemblages that are routinely
collected. Example evaluation questions are:
What level of resolution is used for taxonomy and related biological attributes?
How many assemblages are monitored?
What training and certifications are required for persons identifying organisms?
What are the enumeration and identification QA/QC procedures?
To score highly in this element, at least two assemblages should be used to more completely
assess the condition of the entire aquatic community, and organisms should be identified to the
finest practicable level of resolution. For example, for benthic macroinvertebrates this includes
genus and/or species for key groups, and for fish it would include species resolution in
accordance with the American Fisheries Society nomenclature (Nelson et al. 2004).
Furthermore, staff who identify collected organisms should be formally trained and certified.
Frequently Asked Questions
Question: What is the best taxonomic level of identification?
Answer: The best level of taxonomic identification will vary depending on purpose of assessment and other
considerations, such as the number of genera within each family in a region (Hawkins and Norris 2000b). Typically,
species level is more responsive to impacts from stressors, but coarser level taxonomy can produce more precise
indices (Hawkins 2006). The current ability to accurately and precisely achieve species level identification varies
with the assemblage. Fish, diatoms, and macrophytes can usually be identified to species, whereas
macroinvertebrates can usually be identified to genus. Lower levels of identification can improve one's ability to
estimate stress-response relationships but only if that lower level of identification is not associated with a
substantial increase in the uncertainty of the identifications (Stribling et al. 2008; Buss and Vitorino 2010).
Question: What is the best assemblage to assess biological condition?
Answer: Assemblages comprise different numbers and kinds of species that, in turn, differ in their sensitivities to
stressors and also their occurrence and sensitivity by the water body type. The type of water body being assessed and
its location (i.e., position in the landscape or river continuum) can influence the selection of assemblages to sample.
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The Biological Assessment Program Review February 2013
For example, small primary headwater streams (<1-10 km2 catchment) typically have low fish species diversity, and
development offish indices can be challenging (McCormick et al. 2001; Hitt and Angermeier 2011). As such, assessing
amphibian assemblage in these stream types is an alternative (e.g., Fausch et al. 1984; Moyle and Randall 1998;
Whittier et al. 2007a, 2007b; Ohio EPA 2012). For wetlands, emergent macrophytes are the dominant macrobiota
and are typically used for assessing wetlands (e.g., Fennessy et al. 2007), but they have also been used in rivers
(Moore et al. 2012). Assemblages might also vary along the length of a waterway. For example, preferred
assemblages for the Upper Mississippi River include fish, macroinvertebrates, and submerged aquatic macrophytes
in the impounded portions but fish and macroinvertebrates in the open river reaches (Yoder et al. 2011).
Question: Level 4 requires 2 or more assemblages. What could the mix of assemblages include?
Answer: The mix of assemblages should be complementary rather than redundant in terms of their ecological,
ecophysiological, and ecotoxicological properties (i.e., not represent the same trophic level or have the same
habitat requirements). Assemblages vary in importance across water body types and respond differently to given
stressors. They also respond to different intensities of the same stressor which, in turn, affects assessments of
condition (e.g., Carlisle et al. 2008; Smucker and Vis 2009). For example, one approach might be to strike a balance
among trophic levels: one or more animal assemblage (e.g., benthic macroinvertebrates, fish, zooplankton,
benthic infauna [in estuaries]) and one plant assemblage (e.g., emergent macrophytes, floating/submerged
macrophytes, periphyton, phytoplankton).
Question: Why are two or more assemblages recommended for a Level 4 program?
Answer: Measuring the response of two or more biological assemblages along a gradient of stress provides
increased confidence in the program's capability to detect effects of stressors on aquatic life. There are multiple
pathways in which stressors might affect the biota, and a more comprehensive measure of the biotic community
provides greater confidence that these effects will be detected.
Examples of the responses of different assemblages to stressors include:
Certain species of benthic macroinvertebrates have demonstrated consistent and measurable responses
to metal toxicity. Clements et al. (2000) used cumulative criterion units to quantify metals concentrations
in 95 sites in the Southern Rocky Mountain ecoregion, and they observed changes in the benthic
macroinvertebrate assemblage to different levels of metals. The authors showed that highly
contaminated sites had significantly lower densities of scrapers and predators and also lower in
abundance and species richness of mayflies. Highly contaminated sites also had decreased abundance of
mayflies, caddisflies, and stoneflies (i.e., ephemeroptera, plecoptera, trichoptera [EPT] taxa).
A shift in species composition can signal changes in water quality. When associated with changes in levels
of individual or categories of stressors, this information can be used to support identification of probable
causes of biological impairment (e.g., Carlisle et al. 2008). For instance, a shift in benthic groups from
those that filter the water for food to those that graze the sediments have been correlated with increase
in suspended sediment load in a stream or river in absence of other stressors (Kaller and Hartman 2004).
Carlisle et al. (2008) found that fish and macroinvertebrates in Appalachian streams were most sensitive
to agriculture and urban land uses, while diatoms were most sensitive to chemical changes associated
with mining.
An initial increase in water column algae and shift in species composition can be an indicator of early
nutrient enrichment (McCormick and Cairns 1994). Benthic diatoms have long been used as indicators of
chemical water quality (e.g., Patrick 1949), and recent developments include quantitative models that
infer water quality conditions from the observed diatom assemblage (e.g., Pan et al. 1996; Kelly 1998;
Potapova and Charles 2003; Ponader et al. 2008; Danielson et al. 2011).
The presence of lesions and tumors on fish can be caused by pulp and paper mill discharges (Flinders et
al. 2009), Pharmaceuticals (Kang et al. 2002; Lovy et al. 2007), and other types of chemicals or
industrial/municipal discharges (Yoder and Rankin 1995b; Yoder and DeShon 2003). Dyer and Wang
(2002) examined upstream and downstream data from 221 wastewater treatment plants in Ohio and
observed impairments in fish communities downstream of large treatment plants.
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The Biological Assessment Program Review February 2013
Multiple assemblages were evaluated in 268 Appalachian streams, and both fish and macroinvertebrate
indices were responsive to urban and agriculturally influenced streams. Diatom assemblages were
responsive to mining influence (Carlisle et al. 2008).
Question: How do we get taxonomic certification?
Answer: For some assemblages (algae, fish), professional certification of an individual's ability to accurately and
precisely identify taxa is not available. However, because the accurate and precise identification of aquatic
organisms is the foundation for biological assessment and monitoring programs for lakes, streams, rivers, and
wetlands, certification programs are being developed. For macroinvertebrates, The Society for Freshwater Science
recognized this issue a decade ago and has implemented a certification program for those professionals who
identify macroinvertebrate assemblages for use in assessing aquatic habitats in North America. This program was
designed to certify that trained and skilled persons are providing credible and reliable aquatic macroinvertebrate
identifications at the genus and/or family level. The certification program tests a candidate's knowledge and skills
in aquatic macroinvertebrate taxonomy and provides the successful applicant with a certificate of proficiency.2
Selected states might also offer certifications that address taxonomic and other biological assessment skills and
qualification. For example, Ohio offers certification as a Qualified Data Collector under the Ohio Credible Data Law.
Three levels are offered: Levels 1, 2, and 3. Level 3 is required for acceptance of data by Ohio Environmental
Protection Agency (Ohio EPA) for CWA section 303(d) listing and use designation assignments under the Ohio
Water Quality Standards (WQS). The certification is obtained by completing a required training class and then
completing performance-based testing for fish (including habitat assessment) or macroinvertebrate assemblage
assessment. Certification is also available for the Primary Headwater Habitat assessment methodology and for
chemical/physical sampling. Additionally, California has developed a process to document the quality of the
taxonomic identifications directly. Re-identification of a percentage (typically 10 percent) of taxonomic data by a
QC laboratory is routinely required of most projects in California. Summaries of discrepancies are stored with the
original data, providing users of the final data set with direct information about the quality of the original data,
much as QA batch data provides information about chemistry analyses. In effect, California audits the data instead
of the data providers. California also requires that taxonomists who provide data for the state be active members
of the Southwest Association of Freshwater Invertebrate Taxonomists and follow its standard taxonomic effort
protocols and reporting standards.3
Question: What is DNA barcoding, and is there potential for future application in biological assessments?
Answer: DNA barcoding is a technique by which organisms (fish, macroinvertebrates, macrophytes, algae) can be
catalogued into species based on the nucleotide sequence of one or more gene (e.g., the mitochondrial c oxidase I
gene for fish and macroinvertebrates). A recent approach to characterize the composition, and possibly the health
of communities, is integrating DNA barcoding with metagenomics. Metagenomics refers to the technique
developed to sequence all genetic material present in an environmental sample (soil or water). Moreover, next
generation sequencing technology is allowing for the DNA of all species in a sample to be isolated and sequenced
at once (i.e., resulting in a metagenome). Once a metagenome is obtained, sequencing of a specific gene region
(barcoding) allows one to distinguish the species composition of organisms at a specific location. However, this
approach cannot currently provide information regarding the relative abundance of the species present in the
collections, which is an important factor in using species level data for water quality monitoring. One long-term
goal of the DNA barcode approach is to link biodiversity with existing knowledge of species susceptibilities and
tolerances to environmental stressors so that one can describe and evaluate the condition of a community given
its biological signature.
2 http://www.nabstcp.com/
3 http://swamp.mpsl.mlml.calstate.edu/resources-and-downloads/standard-operating-procedures
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2.1.7 Sample Collection (Element 7)
(Lowest) 1.0
2.0
3.0
4.0 (Highest)
Approach is cursory
and relies on operator
skill and BPJ. Training
limited to that which is
conducted annually for
non-biologists who
compose the majority
of the sampling crew.
Methods are not
systematically
documented as
standard operating
procedures (SOPs).
Textbook methods are used
without considering the
applicability of the methods
to the study area. SOPs to
specify methods but
methods are neither well
documented nor evaluated
for producing comparable
data across agencies. A
cursory QA/QC document
might be in place. Training
consists of short courses
(1-2 days) and is provided
for new staff and
periodically for all staff.
Methods are evaluated
for applicability to study
area and refined (if
needed). Detailed and
well documented SOPs
are updated periodically
and supported by in-
house testing and
development. A formal
QA/QC program is in place
with field replication
requirements. Rigorous
training required for all
professional staff.
Same as Level 3, but
methods cover multiple
assemblages. A field
audit of sampling crews
is performed annually to
ensure that protocols
and proper sample
handling/documentation
are followed.
The sample collection technical element consists of standard operating procedures (SOPs) used
to collect and preserve biological samples and take field measurements. Standardized and well-
tested field methods minimize the variability in biological samples associated with differences in
sampling procedures. A robust QA/QC system provides assurance that SOPs are followed.
Numerous studies have demonstrated that the field methods used can have strong effects on the
characteristics of the collected organisms. For example, samples collected in slow water,
depositional areas provide a different set of taxa compared with samples collected in riffles
(Parsons and Norris 1996). As such, for benthic macroinvertebrates, sampling protocols should
specify how different habitats in a stream reach are selected for sampling (Gerth and Herlihy
2006; Rehn et al. 2007). Similarly, greater sampling effort (e.g., more time spent collecting) results
in larger numbers of individuals and taxa. Use of different sampling equipment (e.g., kicknets vs.
Surber samplers) alter the characteristics of the collected assemblage (e.g., Stark 1993; Cao et al.
2007; Cao and Hawkins 2011).
Scores for this technical element are based on the extent of standardization and evaluation of
field sampling methods and the completeness of the QA/QC system. Example evaluation
questions are:
Are standardized methods used to select sampling locations (e.g., single or multiple
habitats, transects) within a selected site and to collect and preserve samples?
How is QA/QC incorporated in sample collection?
Biological assessment programs that score highly for this technical element have developed well-
defined and rigorous SOPs that specify details of the collection (e.g., where samples are collected,
what sampling equipment should be used, when samples should be collected, how samples
should be preserved). The QA/QC system should provide for regular audits of field crewand
replication of samples at a certain proportion of sites, assign responsibility, define personnel
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The Biological Assessment Program Review
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qualifications, establish protocols, define preventative and corrective action, provide information
tracking, and ensure that study objectives are met (USEPA 1995; Stribling et al. 2008). Voucher
specimens are retained to verify the accuracy of taxonomic identifications.
Frequently Asked Questions
Question: How does sample collection influence the rigor of a biological assessment?
Answer: Sample collection is the genesis of biological assessment data; therefore, how it is designed and executed
influences the ability of a biological assessment to adequately and accurately describe biological quality. However,
biological assessment sample collection should be sufficiently cost-effective so as to produce a sample with 2-3
hours' effort in the field.
Question: How do I know which method is best for my biological indicator (Figure 2-6)?
Answer: Methods should have a well-developed SOP, and all field personnel should be trained by qualified
professionals. The SOP should minimize the decisions that need to be made in the field, and the training should
provide guidance for how to handle unusual situations. If well-developed SOPs and training are done by qualified
professionals with appropriate checks and/or audits in place, the actual sampling could be done by more junior
personnel under the direction of senior level staff. This type of apprenticeship or mentoring is important for
maintaining consistency in sample collection and minimizing variability due to who is doing the sampling at any
one location and/or time.
Figure 2-6. Stream sampling methods.
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2.1.8 Sample Processing (Element 8)
(Lowest) 1.0
2.0
3.0
4.0 (Highest)
Organisms are sorted,
identified, and counted
in the field using
dichotomous keys.
Organisms are sorted,
identified, and counted
primarily in the field by
trained staff. Adequate
QA/QC is not possible. For
fish, cursory examination
of presence and absence
only. Agency SOPs not
developed or published.
All samples (except for
fish) are processed in the
laboratory. A formal
QA/QC program is in
place. Rigorous training is
provided. Voucher
organisms are retained for
ID verification. SOPs are
published and available to
others.
Same as Level 3, but
applied to multiple
assemblages.
Subsampling level is
tested. Presence offish
deformities, erosions,
lesions, tumors (DELT)
and other anomalies are
quantified and
documented.
Sample processing refers to the protocols (i.e., SOPs) that are followed to subsample, sort,
identify, and count the organisms collected from a water body. These protocols include the
specific methods for identifying organisms (e.g., by employing established keys), for training of
the personnel who count and identify the organisms, and for QA/QC. Consistent protocols for
sample processing can minimize the potential that differences in sample processing cause
differences in site assessments.
Protocols for subsampling, including how the subsample is selected and how many organisms
are counted should be specified. For most assemblages, it is infeasible to identify all the
organisms in the sample, and, therefore, a subsample of the collected organisms is identified
and counted. In general, the more organisms that are identified, the more accurately and
precisely one can characterize the structure of the biological assemblage (e.g., Barbour and
Gerritsen 1996; Ostermiller and Hawkins 2004; Cao and Hawkins 2005; Cao et al. 2007).
However, sample processing costs increase with subsampling effort, so the relative benefits of
increased subsampling effort versus processing costs should be considered and documented.
The most appropriate protocols can depend on the assemblage that is collected. For example,
macroinvertebrates are more effectively sorted and identified in the laboratory (Nichols and
Norris 2006), whereas fish are typically identified and counted in the field prior to returning
them to the water body. (Note that when field identifications are used, voucher specimens
should be retained for QA in the laboratory.) Similarly, the presence of deformities, erosions,
lesions, and tumors (DELT) usually can only be assessed with fish samples.
Scores for this technical element are based on the degree to which sample processing is
standardized, and the degree to which QA/QC procedures are both documented and
implemented. Example evaluation questions are:
Are standardized methods for sample processing in place?
Do methods include processing macroinvertebrate and algae samples in the laboratory,
retaining voucher specimens for fish, and using a formal QA/QC program?
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Is the increased accuracy and precision of more intense subsampling effort for
macroinvertebrates and algae relative to the costs of subsampling documented?
For fish, does the program record DELT and other anomalies?
Programs that score highly on this technical element process macroinvertebrate and algae
samples in the laboratory, count DELT anomalies on fish, retain voucher specimens, and use a
formal QA/QC program. The process used to select subsampling effort for macroinvertebrates
and algal assemblages is documented, and it is sufficient for accurate and precise
characterizations of assemblage structure.
Frequently Asked Question
Question: How does the level of macroinvertebrate subsampling affect the results of biological assessment?
Answer: In general, precision of site-specific estimates of taxon richness might improve with both sampling and
subsampling effort. However, there may be diminishing returns for increasing subsample effort, and various
studies have suggested that subsampling more than 500 macroinvertebrate organisms yields little or no additional
precision or accuracy (e.g., Barbour and Gerritsen 1996; Ostermiller and Hawkins 2004; Cao and Hawkins 2005;
Cao et al. 2007). The costs of increased sampling and subsampling effort at single sites needs to be considered in
the overall program design with the information expected to be gained from more extensive sampling (increased
number of sites and sample density). Depending on the questions to be answered, increased subsampling effort
might increase precision and power for before-after and upstream-downstream investigations, while increased
extent of sites might increase power for statewide status and trends investigations.
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2.1.9 Data Management (Element 9)
(Lowest) 1.0
2.0
3.0
4.0 (Highest)
Sampling event data
organized in a series
of spreadsheets (e.g.,
by year, by data-
type). QA/QC is
cursory and mostly
for transcription
errors. Might be
paper files only.
Databases for physical-
chemical, and
biological data, and
geographic information
exist (Access, dBase,
Geographic
Information System
[GIS], etc.) but are not
linked or integrated.
Data-handling methods
manuals are available.
QA/QC for data entry,
value ranges, and site
locations. A
documented data
dictionary defines data
fields in terms of field
methods and data
collection.
Relational databases that
integrate all biological,
physical, and chemical
data (Oracle,SQLServer,
Access, etc.). Validation
checks that guard against
inadvertently storing
incorrect or incomplete
sampling data. Fully
documented and
implemented QA/QC
process. Structure
provides for data export
and analysis via query
includes dedicated
database management.
Fully documented data
dictionary. Access to all
databases is available for
routine analysis in support
of condition assessment.
Same as Level 3 adding
automated data review and
validation tools. Numerous
built-in data management and
analysis tools to support
routine and exploratory
analyses. Ability to track history
of changes made to the data.
Ability to control who has
privilege to change, update, or
delete data. Data import and
export tools. Integrated
connection to GIS showing
monitored sites in relation to
other relevant spatial data
layers. Fully documented
metadata according to
accepted database standards.
Reports on commonly used
endpoints are easily retrieved
(e.g., menu driven).
The data management technical element evaluates the processes and systems that are used by
a monitoring program to store and access collected data. A reliable, well-designed, and quality-
assured database and management system is fundamental to a program's ability to effectively
use monitoring information to assess environmental problems and allows historical data to be
used to evaluate trends and provide historical context. Proper data management ensures that
the appropriate data can be retrieved and analyzed when necessary and with ease of access,
and that historical data are archived in a data repository to protect against data loss
(e.g., Michener and Jones 2012).
Proper data management also requires documented metadata, that is, data about the data.
Metadata documents are the who, what, why, where, when, and how of the data in the
database, so it would include documentation of methods, units, design, objectives. The metadata
ranges from methodological description of the study (or studies) to the data dictionary describing
fields in the database. Metadata can be coded into Ecological Metadata Language, a metadata
specification developed for ecology, based on work sponsored by the National Science
Foundation (The Knowledge Network for Biocomplexity; http://knb.ecoinformatics.org/index.jsp).
Scoring of this technical element is based on the degree to which data management systems
permit the program to retrieve data in formats that are useful for conducting analyses and
supporting decision making. A low score in this element would be associated with simple
spreadsheet storage of monitoring data. Higher scores would be associated with data stored in
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a relational database allowing integration with spatial data and providing stakeholders with
Web access. Also, the methods used for archiving data and for making the data available to
outside users are considered. Example evaluation questions are:
Are data storage and analysis programs in place to access data, determine data quality,
and manipulate the data to evaluate the relationship between measures of stressors or
categories of stressors with biological assemblage response?
Does data management include comprehensive and integrated storage of biological
assessment, physical, chemical, WET, and watershed observations, such that these can
be integrated with respect to space and time?
For a program to score high on this technical element, all monitoring data are stored in a
relational database allowing integration with spatial data and providing users and stakeholders
with Web access to access raw and summary data. Transparent and well-documented QA/QC
procedures are in place for data storage and retrieval, including protocols for tracking changes
in taxonomic nomenclature over time. All relevant data collected by the agency are in one
integrated database system.
Frequently Asked Questions
Question: How do I know what type of data management system I need?
Answer: Data organization and management allows users to perform assessments and reorganize and summarize
data according to analysis needs, including exploratory analyses, index development, and more advanced
research. Use of spreadsheets is the minimum level of an electronic database management system, but
spreadsheets are deficient in error checking and data integration, and they are limited in the amount of
information that can be stored. A relational database addresses these shortcomings. A thorough QA/QC check on
the database ensures a "clean" data set for use throughout an agency's program. A small relational database
management system (RDBMS) such as Microsoft Access could serve as a logical step from spreadsheets to a more
sophisticated relational database. These smaller systems can be used to develop a biological assessment database
that includes most of the relational data integrity and validation features of a larger RDBMS. Most large RDBMS
are installed on a server that provides options for making the database available through a network or Internet
connection. Larger RDBMS are usually installed and administered by an agency's information technology (IT)
department. IT departments can help program managers identify qualified professionals to assist with creating a
custom database to meet the data management and analysis needs of biological assessment programs.
When developing a relational database, it is important to recognize that data access depends on creating and
running queries, which must be properly programmed to extract appropriate data, and to make extracted data
tables available to outside users as flat files.
Question: If I'm able to use electronic spreadsheets or even a small RDBMS such as Microsoft Access, why do I
need a data dictionary (metadata)?
Answer: A well-documented data dictionary defines not only how the data in a particular field relate to field
operations and data collection, but it specifies how those values are stored and validated. Creating a well-
documented data dictionary requires the data manager to address questions ranging from fairly simple to more
complex. For example, are the data numeric or text? Are they allowed to be null? The answers to these questions
might show that multiple types of data are being stored in one field and should be separated. Answering these
questions helps to bridge the gap between using spreadsheets and moving toward a more robust data
management system.
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2.1.10 Ecological Attributes (Element 10)
(Lowest) 1.0
2.0
3.0
4.0 (Highest)
Biological program
relies solely on the
evaluation of the
presence or absence of
targeted or key species.
No rationale is provided
for selection of
indicators. Assessment
endpoints and
ecological attributes
are not defined.
Biological program based
on "off the shelf indicators
for one biological
assemblage. Rationale for
selection of indicators is
partially documented.
Generic assessment
endpoints and ecological
attributes are defined but
not specifically evaluated
for state or regional
conditions.
Biological program based
on well-developed
ecological attributes for one
biological assemblage.
Rationale for attribute
selection is thorough and
well-documented. Explicit
linkage is provided between
management goal,
assessment endpoints, and
ecological attributes.
Same as Level 3, but
biological program
based on well-
developed ecological
attributes for two or
more biological
assemblages (e.g.,
faunal, flora) for more
complete assessment
of the members of an
aquatic community.
The objective of the 1972 CWA is to "... to restore and maintain the chemical, physical and
biological integrity of the Nation's waters." However, the CWA does not provide an explicit
description of biological integrity nor specify ecological assessment endpoints and scientific
methods to measure integrity. One description of biological integrity is "a balanced, integrated,
and adaptive community of organisms having a composition and diversity comparable to that of
natural habitats of the region" (Frey 1975; Karr and Dudley 1981). Primarily based on this
definition or on later refinements (Karr and Chu 2000), states and tribes have used biological
assessments to measure the condition of biological communities relative to biological integrity.
This technical element evaluates how well a biological assessment program has selected and
operationally defined assessment endpoints that adequately represent biological integrity.
Assessment endpoints are measurable characteristics, or attributes, representative of a
management goal (USEPA 1998). The attributes provide the basis for development of
quantitative measures (e.g., biological indices) to assess attainment of the management goal.
Selection of attributes to measure biological integrity includes consideration of their ecological
relevance, susceptibility to known or potential stressors, and relevance to the management
goal (USEPA 1998). Ecologically relevant attributes might be identified at any level of
organization (e.g., individual, population, community, ecosystem, landscape). Typically states
and tribes have identified species diversity and abundance as ecologically relevant attributes
for measuring biological integrity and have developed biological indices using measures of
taxonomic diversity and completeness, composition, trophic state, and trophic composition.
Full consideration of all three selection criteria (e.g., ecological relevance, susceptibility to
known or potential stressors, relevance to management goal) provides the best foundation for
development of biological indices to measure biological integrity. Poorly defined attributes can
lead to miscommunication and uncertainty in applying assessment results to making a
judgment on attainment of the management goal. For example, susceptibility of an ecological
attribute to stressors and/or levels of human disturbance in the environment is important in
selecting attributes but should be considered in the context of how well an attribute can
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represent the management goal. Otherwise, an attribute could be selected that leads to a biotic
index that provides a robust and precise measure of human disturbance but not an accurate
measure of biological integrity.
Scientists from EPA, U.S. Geological Survey, state and tribal agencies, and academic institutions
jointly developed a conceptual scientific model that describes the response of 10
ecological attributes to increasing anthropogenic stress (Davies and Jackson 2006, Table 2-3).
This model, the Biological Condition Gradient (BCG), is based on a suite of ecological attributes
used by different state and tribal biological assessment programs across the country. The BCG
was developed to provide a common framework for interpretation of biological assessments
regardless of methods or regional differences. The ecological attributes of the BCG might serve
as a template, or starting point, for states and tribes to consider in their selection of attributes.
Scoring for this technical element is based on how a biological assessment program has
selected and operationally defined ecological attributes to assess biological integrity and then
used them as the basis for development of biological indices. Because the condition of a
biological community can be more confidently assessed with more than one biotic assemblage,
the number and type of assemblages are considered in the evaluation (e.g., Carlisle et al. 2008).
Example evaluation questions are:
Are ecological attributes defined that provide for development of biological indices to
measure attainment of biological integrity? If so, what are the ecological attributes and
what is the basis for their selection?
What aquatic assemblages are assessed?
How is the linkage between biological integrity, ecological attributes, and biological
indices defined, tested, and documented?
Programs that receive the highest scores for this technical element have well-developed
ecological attributes for two or more assemblages. The linkage between biological integrity,
assessment endpoints, ecological attributes and the resulting biological indices is explicit and
documented.
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Table 2-3. Biological and other ecological attributes used to characterize the BCG
Attribute
Description
I. Historically documented,
sensitive, long-lived, or regionally
endemic taxa
Taxa known to have been supported according to historical, museum, or
archaeological records, or taxa with restricted distribution (occurring only
in a locale as opposed to a region), often due to unique life history
requirements (e.g., sturgeon, American eel, pupfish, unionid mussel
species).
II. Highly sensitive (typically
uncommon) taxa
Taxa that are highly sensitive to pollution or anthropogenic disturbance.
Tend to occur in low numbers, and many taxa are specialists for habitats
and food type. These are the first to disappear with disturbance or
pollution (e.g., most stoneflies, brook trout [in the east], brook lamprey).
III. Intermediate sensitive and
common taxa
Common taxa that are ubiquitous and abundant in relatively undisturbed
conditions but are sensitive to anthropogenic disturbance/pollution. They
have a broader range of tolerance than highly sensitive taxa (attribute II)
and can be found at reduced density and richness in moderately disturbed
sites (e.g., many mayflies, many darter fish species).
IV. Taxa of intermediate
tolerance
Ubiquitous and common taxa that can be found under almost any
conditions, from undisturbed to highly stressed sites. They are broadly
tolerant but often decline under extreme conditions (e.g., filter-feeding
caddisflies, many midges, many minnow species).
V. Highly tolerant taxa
Taxa that typically are uncommon and of low abundance in undisturbed
conditions but that increase in abundance in disturbed sites. Opportunistic
species able to exploit resources in disturbed sites (e.g., tubificid worms,
black bullhead).
VI. Nonnative or intentionally
introduced species
Any species not native to the ecosystem (e.g., Asiatic clam, zebra mussel,
carp, European brown trout). Additionally, there are many fish that have
expanded their range within North America because they have been
introduced to areas where they were not native.
VII. Organism condition
Anomalies of the organisms; indicators of individual health (e.g.,
deformities, erosions, lesions, tumors [DELT]).
VIII. Ecosystem function
Processes performed by ecosystems, including primary and secondary
production; respiration; nutrient cycling; decomposition; their
proportion/dominance; and what components of the system carry the
dominant functions. For example, shift of lakes and estuaries to
phytoplankton production and microbial decomposition under disturbance
and eutrophication.
IX. Spatial and temporal extent of
detrimental effects
The spatial and temporal extent of cumulative adverse effects of stressors,
(e.g., widespread tile drainage and stream channelization throughout an
ecoregion resulting in extirpation of several species of native
macroinvertebrates and fish).
X. Ecosystem connectance
Access or linkage (in space/time) to materials, locations, and conditions
required for maintenance of interacting populations of aquatic life; the
opposite of fragmentation (e.g., levees restrict connections between
flowing water and floodplain nutrient sinks [disrupt function]; dams impede
fish migration and spawning).
Source: Modified from Davies and Jackson 2006.
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Frequently Asked Questions
Question: Are all 10 BCG attributes necessary to characterize biological integrity?
Answer: The selection of attributes might depend on the spatial scale and specific water body being assessed. Each
attribute provides some information about the biological condition of a water body. Combined into a conceptual
model comparable to the BCG, the attributes can offer a more complete picture about current water body
conditions and also provide a basis for comparison with naturally expected water body conditions. All states and
tribes that have applied a BCG for streams, rivers, and wetlands have used the first seven attributes that describe
the composition and structure of biotic community on the basis of the tolerance of species to stressors and, where
available, included information on the presence or absence of native and nonnative species, and, for fish and
amphibians, used measures of overall condition (e.g., size, weight, abnormalities, tumors). Though not measured
directly in state or tribal stream biological assessment programs, the last three BCG attributes of ecosystem
function and connectedness and spatial and temporal extent of stressors can provide valuable information when
evaluating the potential for a stream, river, or wetland to be protected or restored. For example, a manager can
choose to target resources and restoration activities to a stream where there is limited spatial extent of stressors
or there are adjacent intact wetlands and stream buffers or intact hydrology, rather than a stream with
comparable biological condition but where adjacent wetlands have been recently eliminated, hydrology altered,
and stressor input is predicted to increase.
However, for comprehensive water body-wide assessments of large systems like estuaries and coastal ecosystems,
the full suite of attributes might be important for application at both a single habitat scale similar to streams and
for a landscape level assessment that describes the distribution and connectedness of habitats within an
ecosystem necessary for the survival and resiliency of the resident biota (e.g., fish, benthic invertebrates,
migratory water birds, aquatic mammals).
Question: I have a calibrated index. Why do I need to consider the ecological attributes of the BCG?
Answer: The BCG serves as a conceptual model, or framework, for organizing and communicating information on
biological community response to increasing levels of stress in aquatic ecosystems. The BCG was developed in
partnership with scientists from state and tribal biological assessment programs from across the country (Davies and
Jackson 2006). The BCG attributes and levels of condition represent shared, measurable patterns of biological
response to increasing stress condition regardless of location and method. Many of the state and tribal scientists
involved in BCG development had already derived biological indices based on methods and approaches developed in
the 1980s through 1990s (e.g., index of biotic integrity (IBI) for fish [Karr et al.1986]). Therefore, there is both
conceptually and quantitatively a close association between BCG attributes and the biological indices currently used
by many states and tribes. The suite of BCG attributes can serve as a template for reviewing and improving an existing
biological index or for developing a new index.
Question: What is a trait-based approach?
Answer: A trait-based approach predicts patterns of species attributes (i.e., reproductive, physiological,
behavioral) and environmental conditions (Poff et al. 2006; Pollard and Yuan 2010). This approach has not been
consistently applied or formally articulated until the last decade. It is based on sound theoretical concepts, such as
the Habitat Templet Concept, which predicts that habitat and environmental conditions select organisms with
particular life-history strategies and biological traits (Southwood 1977,1988). Many studies have demonstrated
that patterns in the traits of species can be related to environmental conditions (e.g., Townsend et al. 1997;
Richards et al. 1997; Statzner et al. 2005; Van Kleef et al. 2006).
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2.1.11 Discriminatory Capacity (Element 11)
(Lowest) 1.0
2.0
3.0
4.0 (Highest)
Coarse method (low
signal) and detects
only high and low
values. Supports
distinguishing only
extreme change in
biological condition at
the upper and lower
ends of a generalized
stress gradient.
A biological index for
one assemblage is
established but is not
calibrated for water
body classes, regional or
statewide applications.
BPJ based on single
dimension attributes.
The index can
distinguish two general
levels of change in
biological condition
along a generalized
stress gradient.
A biological index for one
assemblage has been
developed and calibrated for
statewide or regional
application and for all classes
and strata of a given water
body type. The index can
distinguish 3 to 4 increments
of biological change along a
continuous stress gradient.
Supports narrative
evaluations (e.g., good, fair,
poor) based on multimetric
or multivariate analyses that
are relevant to the selected
ecological attributes
(Technical Element 10).
Same as Level 3 but
biological indices for two
or more assemblages have
been developed and
calibrated. Additionally,
the indices can distinguish
finer increments of
biological change along a
continuous stress
gradient. The number of
increments that
potentially can be
distinguished is
dependent on water body
type and natural climatic
and geographic factors.
This technical element addresses how a biological assessment program has developed one or
more biological indices based on ecological attributes (Technical Element 10) and the degree of
sensitivity of the indices in distinguishing incremental change along a continuous gradient of
stress. Detailed descriptions of biological change along a gradient of stress can provide detailed
descriptions of a state's designated aquatic life uses for specific water bodies and regions and
lead to biological criteria development. Additionally, depending on the sensitivity, or
discriminatory capacity, of the index, the information can be used to help identify high-quality
waters and establish incremental restoration goals for degraded waters.
The ability of a biological index to measure change along a continuous gradient of stress
includes consideration of the appropriate scale for application of the index (e.g., a specific
water body, class of water body, region, statewide) and defining, and wherever possible,
quantifying overall variability and sources of uncertainty.
The BCG discussed in the preceding section (Technical Element 10) is a conceptual model that
describes measurable increments of biological change along a gradient of stress (Davies and
Jackson 2006). Six general increments of change have been described for each of the BCG's
ecological attributes. The gradient ranges from natural, undisturbed conditions to severely
degraded conditions caused by anthropogenic stresses. These incremental changes can serve as
a template for developing biological indices that represent aspects of biological integrity and
show a predictable, measurable response to increasing levels of stress.
Scoring of this technical element is based on the demonstrated ability of the biological index to
detect increments of change along a continuous gradient of stress. Examples of evaluation
questions are:
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Is the index developed and calibrated at the appropriate scale for its intended application?
Is the index developed and verified by independent data sets?
What is the sensitivity of the index to detect shifts in biological assemblages along a full
gradient of anthropogenic stress?
How well defined, quantified, and documented is overall variability and its sources?
What biotic assemblages are assessed?
Programs that score highly on this technical element have well-developed indices for one or
more assemblages and have demonstrated the ability of their indices to distinguish incremental
levels of biological condition change along a continuous stressor gradient for specific water
body types and regions. Sources of uncertainty are well defined and quantified. For a program
to score at the highest level, well-developed biological indices for two or more assemblages are
used for a more complete assessment of biological integrity.
Frequently Asked Questions
Question: Can an agency's existing biological index be refined rather than replaced to improve discriminatory
capacity?
Answer: As a biological index is further developed, it can be recalibrated and compared with performance of the
previous iteration to compare past and present results. Recalibration of an index or model should be considered,
for example, when sample collection or processing protocols change; classification is refined; level of taxonomic
identification is made more precise; or, the data set is substantially expanded to include longer time-series,
stressor conditions, or reference characteristics. These technical improvements can influence discriminatory
capacity of an index or model.
Developing a quantitative translation between the original and refined index might require a special study where
samples are collected simultaneously using the two protocols (for methodological changes). For example, in New
England, alternative sampling and index methods were run side-by-side at the same sites (Snook et al. 2007). For
minor methodological changes (e.g., taxonomic level, sampling or subsampling effort), analysis could be performed
on samples that are virtually reformatted to provide two samples reflecting each protocol. For example, if
Chironomidae (midges) were previously identified at the family level, but are currently identified at the genus
level, the identifications in new samples could be reset at family level for calculation of the old index. Then
comparisons of old and new indices could be performed on the reformatted and complete samples, yielding old
and new index scores that could be compared through regression or other analyses. This would allow prediction of
one index from the other and comparison of the assessment thresholds.
Question: Are the same increments of measurement expected for all aquatic water body ecotypes or in all regions
of the United States?
Answer: The number of increments that can be distinguished is dependent not only on the water body ecotype
and natural climatic and geographic factors that define the assemblage characteristics, but the effect of
anthropogenic stressors. For example, the sensitivity of an index developed for a forested, high-gradient stream
might support distinguishing five to six increments of change along a continuous stressor gradient while an
intermittent, seasonal, or desert stream might support only three increments. Some of this is due to inherent
natural characteristics of the assemblages and some might be due to current limitations of science and practice.
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2.1.12 Stressor Association (Element 12)
(Lowest) 1.0
2.0
3.0
4.0 (Highest)
No ability to develop
relationships
between biological
responses and
anthropogenic stress.
Site-specific paired
biological and stressor
samples for studies of
an individual water
body or a segment of a
water body (e.g., a
stream reach). Stress-
response relationships
are developed based
on assemblage
attributes at coarse
level taxonomy (e.g.,
family for benthic
macroinvertebrates).
Information might be
used on a case-by-case
basis to inform a first
order causal analysis.
Low spatial resolution for
paired biological and
stressor samples in time
and space across the state
at basin or sub-basin scale
(e.g., HUC 4-8). Stress-
response relationships
developed for one
assemblage using
regression analysis.
Taxonomy at level
sufficient to detect
patterns of response to
stress (e.g., species or
genus for benthic
macroinvertebrates or
periphyton, species for
fish). Relational database
supports basic queries.
Information is frequently
used to inform causal
analysis. Reevaluation of
stress-response
relationships on an as-
needed basis.
High spatial resolution for
paired biological (including
DELT anomalies and other
indicators of organism health)
and stressor samples in time
and space across the state at
watershed or subwatershed
scales (e.g., HUC 10-12). Other
data (e.g., watershed
characteristics, land use data
and information, flow regime,
habitat, climatic data) are
linked to field data for source
identification. Stress -response
relationships are fully
developed for two or more
assemblages, stressors, and
their sources using a suite of
analytical approaches (e.g.,
multiple regression,
multivariate techniques).
Relational database supports
complex queries. Information
is routinely used to inform
causal analysis and criteria
development. Ongoing
evaluation of stress- response
relationships and monitoring
for new stressors is supported.
Stressor association refers to the use of biological assessment data at appropriate levels of
taxonomy to develop relationships between measures of biological response and
anthropogenic stressors, including both stressor and their sources (Yuan and Norton 2003; Huff
et al. 2006; Yuan 2010; Miller et al., 2012). This includes examination of biological assessment
data for patterns of response to categorical stressors (Yoder and Rankin 1995b; Riva-Murray et
al. 2002; Yoder and DeShon 2003). A capability for developing these relationships extends the
use of biological assessments from assessing condition to informing identification of possible
causes and sources of a biological impairment at multiple scales.4
The technical capability to associate biological response with stressors and their sources
affecting aquatic systems requires a comprehensive database that should include biological,
chemical, physical, and WET data and information; detailed watershed and land use
For more information about stressor identification, see EPA's Causal Analysis/Diagnosis Decision Information
System website at: http://www.epa.gov/caddis.
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The Biological Assessment Program Review February 2013
information; locations of discharges; discharge monitoring; Geographic Information System
(CIS) capability to assemble watershed and discharge information and relate them to the
correct sampling sites, etc. Paired biological and other relevant environmental data support
developing quantitative stress-response relationships. A relational database that enables data
export and analysis via query is required to support this function. Since chemical sampling is
often more frequent (several times per year) than biological sampling, the database should be
able to accommodate queries to relate the higher-frequency chemical sampling to lower-
frequency biological sampling. It should also be able to reveal the spatial coincidence of
biological and chemical/physical sampling locations to reveal the extent to which these are
actually paired.
Stressor association, is directly dependent on a high level of technical development of other
elements, particularly the elements for spatial sampling design, taxa and level of taxonomic
resolution, database management, and discriminatory capacity. These elements are important
building blocks for the data collection and analysis needed to more confidently identify
stressors and their sources and to estimate stress-response relationships. For example, the
ability to estimate these relationships relies on paired stressor and response sampling at
appropriate spatial and temporal scales and a level of taxonomic resolution and index
sensitivity sufficient to detect incremental biological changes along a stress gradient. Also, a
relational database that supports complex queries enables efficient and full utilization of data.
A high level of technical development for each of these elements and others provides the
foundation for stressor association.
Scoring for this technical element is based on the degree to which biological assessments are
used to estimate stress-response relationships and discern patterns of response to individual or
categorical stressors. Example evaluation questions are:
Are biological sample collection and stressor sample collection coordinated? What
assemblages are sampled and to what level of taxonomy?
Does the database support analysis of biological responses to individual stressors or
categories of stressors? If so, at which spatial scale(s)?
Is a systematic approach for identifying stressors at biologically degraded sites used? Is
this information used on a routine basis to support identification of probable cause of
the biological impacts and source of the stressors?
Does the database support the continued analysis of biological responses, including
WET, to individual stressors or categories of stressors especially as additional data are
collected and as stressors change over time?
Programs receiving the highest score on this technical element collect data and conduct
analyses that enable the estimation of relationships between biological responses for two or
more assemblages and the dominant stressors in their regions. Data sets are examined to
discern patterns of response to categorical stressors and for source identification. To elucidate
stress-response relationships, the biotic and abiotic data and measurements must be both
temporally and spatially linked in data sets. Within-site variability is characterized and
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appropriately incorporated into the analysis. New monitoring data and information on changes
in land use and new stressors are systematically gathered and evaluated as a part of the routine
monitoring and assessment program so that new stressors and their biological impacts are
detected and stressor-response variables developed accordingly. Information is used to inform
causal analysis and support criteria development. Timely information is also provided to other
water quality programs to meet their information needs on stressor-response relationships and
causal analysis.
Frequently Asked Questions
Question: What biological assessment information can be used as a basis for diagnosing problems?
Answer: Appropriately detailed biological assessment information is needed to discriminate between different
categories of stressors and requires analyses of large data sets to reveal patterns of biological response across
spatial and temporal gradients. To further examine for patterns of biological response to stress, equally detailed
information on stressors, habitat, potential sources, and the natural background condition are also needed.
Question: How does one analyze stress-response?
Answer: There is a large and growing base of literature exploring different approaches to analyzing stress-
response relationships from field data. Methods range from simple regressions to complex multivariate models
and new methodologies (see Legendre and Legendre 1998 for an overview). The objective is to find community-
level diagnostics, also called biological response signatures, which are characteristics of a biological community
and are associated with specific stressors or categories of stressors and can be used diagnostically. In some cases,
these indicators have been used by agencies to identify possible stressors from biological data (Yoder and DeShon
2003; Yoder and Rankin 1995b; Riva-Murray et al. 2002). A further refinement to this approach compares stressor-
specific tolerance values associated with taxa collected at sampling sites with those from an expected assemblage
predicted by a RIVPACS-type model (Huff et al. 2006; Hubler 2008). Additionally, new analytical approaches are
being explored for identifying patterns of biological response to individual stressors, types or categories of
stressors, and/or their sources (e.g., Shipley 2000; USEPA 2000; Oksanen and Minchen 2002; Cade and Noon 2003;
Cormier et al. 2008; Baker and King 2009; King and Baker 2010; USEPA 2010a; Cormier et al. 2013).
Question: What are biomarkers, and can they be used for diagnosis?
Answer: Biomarkers are histopathological or biochemical signatures found in organisms that indicate some
combination of stress, exposure to specific chemicals, or a disease. They are typically assayed from single
individuals, where several individuals from a single site are sampled. They have been used most often in attempts
to diagnose causes of observed impairments or mortality in fish. For example, Ripley et al. (2008) examined
protein expression profiles of smallmouth bass in the Shenandoah River to identify candidate causes of biological
impairment of the river and of several fish kills. They found that fish in the Shenandoah are immunologically
stressed; however, there are multiple candidate causes of the stress (eutrophication, pesticides, agricultural
animal runoff) (Ripley et al. 2008). Biomarkers of exposure to polycyclic aromatic hydrocarbons (PAHs) were
examined in fish in contaminated rivers in Ohio, and they were key in identification of PAHs as one of several
causes of biological impairment in the rivers (Lin et al. 2001; Yoder and DeShon 2003). This example illustrates how
biological assessments in combination with other biological, chemical, or physical information support more
robust causal analysis.
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2.1.13 Professional Review (Element 13)
(Lowest) 1.0 2.0 3.0 4.0 (Highest)
Review is limited to
editorial aspects. No
technical review.
Internal technical
review only.
Outside review of
documentation and
reports are conducted
on an ad hoc basis.
Formal process for technical
review to include multiple
reference and documented system
for reconciliation of comments and
issues. Process results in methods
and reporting improvements. Can
include production of peer-
reviewed journal publications by
the agency.
The professional review technical element is the level to which agency data, methods, and
procedures are reviewed, especially with regard to external stakeholder and scientific peer
reviews. Subjecting documented methods and assessment reports to rigorous scientific peer
review is ultimately the best way to ensure that an agency's data and scientific underpinnings
are credible. Inherently, scientific peer reviews should be conducted in an objective and
independent manner (outside the agency and with no vested interest in the outcome) by
technical and other experts able to provide valid critique and suggestions, and where
recommendations for improvement and refinement are taken in good faith. Validation of SOPs
for all aspects of the assessment and monitoring program by outside experts is an initial step in
establishing confidence in the resulting data. Programs that do not address and implement
critical recommendations fail to benefit from an independent endorsement of their procedures
and assessments.
The scoring for this technical element is based on the level of scientific peer review. Example
evaluation questions are:
Are documented methods and assessment reports subject to a rigorous scientific peer
review process?
What type of peer review is conducted, and how does the agency address review
comments and document its response?
To score high in this technical element, a program will have a formal process for routine
scientific peer review of data and documents. Programs with a high level of rigor ensure that
reviews are done by outside, independent reviewers. The agency will also have an established,
transparent process for documenting and tracking how it responds to comments from
reviewers. Technical approaches might be included in peer review journal articles.
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Frequently Asked Question
Question: Agency documents and reports are subjected to a thorough internal review by managementwhy is
that not sufficient?
Answer: A peer review by technical experts from outside the agency is crucial to validating all aspects of a biological
assessment program. Peer review provides feedback for strengthening a program and validation for the technical
foundation to support water quality management decisions. In particular, publishing biological assessment protocols
through a peer-reviewed process demonstrates a high level of technical rigor and acceptance in the scientific
community.
2.2 Determining the Overall Technical Program Level of Rigor
A technical element's scoring matrix or "checklist"
has been developed to rate or score the key
technical elements according to a four-tiered
narrative description along a sliding scale that
ranges from 1 to 4 (Appendix E). The
checklist is used to evaluate each element and rate
it independently as part of the overall program
evaluation process. The scoring of the individual
technical elements is based on the role of each
element in supporting a biological assessment
program's ability to:
Assess biological condition of a water body in
terms of biological integrity.
Define biological change along a gradient of
stress.
Relate biological response to stressors and
develop stress-response relationships.
EPA recognizes that the components of the various
technical elements are inherently interrelated and
the status or refinement of one element can
influence others. However, focusing on individual
elements first and then aggregating them into a
cumulative rating provides an estimate for the
overall level of rigor of a biological assessment
program. The individual technical element scores
can be used to prioritize specific areas for corrective
actions and improvement, and these are detailed in
Appendix E. The checklist should be completed for
major water body types (e.g., flowing waters, lakes,
*~ The 13 technical elements are evaluated
equally for the purpose of identifying
strengths and areas for improvement.
Clearly, several entail greater level of effort
for development. Many are building blocks
for others. For example, Technical Element
5, Reference Condition, evaluates the
number of reference sites that are available
based on reference site section factors
(Technical Element 4); the degree to which
the reference sites represent natural
environmental gradients (Technical Element
3) and whether the number of sites is
sufficient to support statistical evaluation of
condition and derivation of numeric
biological criteria. Likewise, Technical
Element 12, Stressor Association, is
influenced by whether there is sufficient
spatial resolution (Technical Element 2) and
natural classification (Technical Element 3)
to characterize both natural and stress
gradients as well as number of assemblages
used to measure aquatic life use and detect
stress-response relationships (Technical
Element 6). Fundamental to this element is
an adequate data management system
(Technical Element 9) so that data is readily
accessible and can be manipulated for
complex analysis. The relationships between
the technical elements and level of effort
and sequence for each are part of the
discussion in development of
recommendations and action plan.
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wetlands) with the assemblages used for each water body type noted. Different levels of
biological assessment rigor might be evident among the different water body types and
assemblages sampled, which is important for the water quality agency to determine and
reconcile for management purposes.
It is important that the determination of the level of rigor be done with care to avoid an
erroneous classification of the program. The evaluation of each technical element and the
overall level of rigor of a biological assessment program should be done with the direct input of
the state or tribal manager, supervisor(s), and technical staff. Documentation about the
biological assessment program will be needed to complete various aspects of the checklist. The
checklist should be completed for each water body ecotype as appropriate for the natural
classification framework (e.g., lake, flowing waters, wetland, and per ecological region or other
classification factors such as elevation) that the water quality agency routinely monitors. It is
possible that different levels of rigor are being implemented for the different water body
ecotypes within the jurisdiction of the state or tribe. The overall program score provides an
indication of a biological assessment program's capability to derive biological criteria, describe
biological change along a gradient of stress and develop response-stress relationships (Table 2-
4)-5
Table 2-4. Scoring associated with technical element levels of rigor
Level of Rigor
4
3
2
1
CE Score
49-52
43-48
34-42
13-33
% CE Score6
>93.2
> 81.7-93.1
> 66.4-81.6
24.0-66.3
The central tendency of a biological assessment program's technical capability for each
technical element is evaluated to arrive at a score. A score for one element might end up as a
3.5 if its central tendency is comparable to the technical capabilities of Level 3 but it has some
technical characteristics of a Level 4 program and none of Level 2. It is important to emphasize
that the evaluation process is intended to guide program development building on existing
technical capabilities and addressing the gaps revealed in the review, rather than being viewed
as a report card.
Summing the individual scores of the 13 technical elements provides a raw score for the
biological assessment program with a range of 13-52. This score is then converted to a percent
score by dividing the raw CE score by 52. The thresholds for determining the four levels of rigor
Because the overall score is the result of the summation of individual scores for the 13 separate elements, the
overall score does not establish minimum expectations regarding a state's ability to make decisions in context of
different CWA regulatory programs. At all levels of technical development, biological assessment information can
be used to support water quality decisions.
6 The percent CE score is calculated based on 0.5 increments between CE raw scores.
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are based on an allowable deviation from the maximum cumulative score of 52 across all
13 elements (Table 2-5). These thresholds correspond with improved program capabilities to
detect shifts in biological assemblages along a gradient of stress, more comprehensively assess
the biotic community, detect the suite of stressors impacting the biota, and quantify stressor-
response relationships. For Level 4, there is a 3-point deviation or departure, a 9-point
departure for Level 3, and an 18-point departure for Level 2. Deviations greater than 18 result
in a Level 1 assignment.
Table 2-5. Allowable deviation of technical elements scores for each of the four levels of rigor
Level of Rigor
4
3
2
1
Departure from maximum
cumulative score
-3
-9
-18
greater than -18
The levels of rigor are based on departures across the 13 technical elements as opposed to a
strictly linear interpretation across the four narrative descriptions of each element (e.g., 3 x 13
= 39 as the maximum score for Level 3, 2 x 13 = 26 as the maximum score for Level 2). As such,
the delineations of the four levels are based on the aggregate degree of departure across all
13 elements and in recognition that the overall level of rigor is an aggregate reflection of all
13 elements combined. It also recognizes the scoring across the four element narratives as an
ordinal gradient as opposed to rigid and discrete categories. Based on the pilot evaluations,
state and tribal biological assessment programs might exhibit characteristics of adjacent
categorieshence the sliding scoring scale in 0.5 point increments.
The pilot testing done with states in 2002-2004 and follow-up evaluations conducted with
selected states through 2010 show a congruence between the level of rigor and the formal
adoption of numeric biological criteria and refined aquatic life uses in WQS (Table 2-6). Of the
three states that have adopted numeric biological criteria and/or refined aquatic life uses in
their WQS, two are Level 4 programs and one is 0.5 point from Level 4. Of the remaining five
Level 3 states, three were considering developing numeric biological criteria and refined aquatic
life uses, and each was expecting to continue technical development towards Level 4 as a result
of ongoing technical and program developmental efforts. For states either achieving or
developing a Level 4 program, coordinated biological, WET, chemical, and physical assessments
and implementation of stressor identification as part of the water quality management
program were either in place or being planned for.
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Table 2-6. State Pilot Biological Assessment Reviews: Correspondence of the level of rigor to
adoption or development of refined aquatic life uses and/or biological criteria in state WQS
CE Level (n)
4(2)
3(5)
2(14)
1(0)
Refined Aquatic Life Uses
&Biological Criteria in
WQS7
2
1
0
0
Refined Aquatic Life Uses &
Biological Criteria in
Development
3
0
0
Not Developing Refined
Aquatic life Uses &/or
Biological Criteria in WQS
2
14
0
The guiding principles of the technical elements approach are intended to help state and tribal
monitoring and assessment programs achieve levels of standardization, rigor, reliability, and
reproducibility that are reasonably attainable under current technology and available funding
(Yoder and Barbour 2009). While the assignment of a biological assessment program to one of
the four levels of rigor has meaning and utility as a summary tool for assessing overall progress,
how a state or tribe responds to the evaluation results is the critical action. For Level 4
programs, the focus is on program maintenance and how the program is incorporating new
advances in the science and technology of biological assessment. In contrast, for Level 1, 2 and
3 programs, the focus is on the technical developments that are either already underway or
that need to take place to meet the agency's needs for biological assessment data and
information.
includes biologically-based refined uses only.
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The Biological Assessment Program Review February 2013
CHAPTER 3: THE PROGRAM EVALUATION PROCESS
3.1 Introduction to the Evaluation Process
The biological program review is a systematic process to evaluate the technical capabilities of a
state's biological assessment program and to identify next steps for overall program
improvement. In this process, an expert reviewer conducts in-person interviews with the water
quality agency and guides discussions with water quality agency managers and staff. Regional
U.S. Environmental Protection Agency (EPA) managers and/or staff typically participate in the
review and provide support to the process. The number of water quality agency personnel
engaged in the review usually varies depending on the topic of discussion. The biological
assessment and Water Quality Standards (WQS) program managers and technical staff are
present throughout the review and constitute the core technical review team. Managers and
staff from other programs within the agency, as well as other state agencies that conduct
biological monitoring and assessments, might participate for the full workshop or engage for
specific topics, overall summary discussions, and the concluding session (see Figure 3-1).
The expert reviewer acts as a facilitator to provide an objective perspective on a state's
biological assessment program and to lead the review process, including the scoring of the
individual technical elements and writing the results (e.g., the technical memorandum).
Important considerations for selection of an expert reviewer include:
Expertise in biological assessments and aquatic ecology.
In-depth experience in conducting biological assessments and data analysis.
Practical and applied knowledge of state and tribal biological assessment programs.
Ability to facilitate the review and complete the technical memorandum objectively.
The review is composed of two parts (Figure 3-1). The first part of the review provides an
overview of the biological assessment program and involves discussion of many aspects of the
biological assessment program and how that information is used by different water quality
programs. The second part of the review, the technical elements review, is the evaluation by
the core review team of the technical rigor of the biological assessment program. The first part
of the review focuses on program background to provide context for a state or tribal water
quality management program to evaluate the type and quality of biological assessments
appropriate to answering specific information needs. Using the review results as a road map, a
state or tribe can develop a technical program to support its intended use of biological
assessments. This is why the first part of the review process includes discussion of how a
program functions and whether the biological assessment program is providing the type and
level of information needed by the state or tribe. This discussion sets the stage for the technical
evaluationthe determination of biological assessment program strengths and limitations in
context of an agency's water quality management program information needs.
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Introduction
Presented by Facilitator
' General purpose and overview of
bioassessment evaluation process
' Review process, expected outcome,
and products
Discussion
Part 1: Overview of
Biological Assessment Program
Presented by Agency Managers and Staff
1
r ^r
Monitoring and Reporting and
Assessment Listing
Design and methods
Assessmenttechniques
Data process and management
Benchmarks/thresholds
Resources
Delineation of
impaired/threatened waters
Assessment process
305(b) condition reports
303(d) listing of impaired waters 1
^T
Water Quality
Standards
CurrentWQS issues
j Designated aquatic life uses
and biological criteria
1 Antidegradation and use
attainability analysis
^
Assessment and
Integration Issues
Surface water indicators
b Program integration
(e.g.,402NPDES program, 319
nonpoint source program, etc.)
i -Training
1 1 1 1
T
Agency Self Tests
Small Groups -Agency Managers and Staff
Evaluate technical program performance for 5 management scenarios
' Discuss how well technical program provides information needed by state
water quality agency
Part 2: Technical Elements Review
Facilitated by Reviewer
Technical Elements
Evaluate each technical
element using scoring guide
and checklist
Document rationale for score
Identify tasks to improve score
Program Evaluation
Calculate level of program rigor
using scoring matrix
Discuss added value of
incremental improvements in
technical elements
i i
Concluding Session
All participants
' Revisit how well current biological assessment program addresses water
quality agency information needs
Identify priorities and rationale for improving technical program
Discuss outstanding questions, issues and concerns about evaluation
results
> Determine process and steps to finalize evaluation results (e.g., technical
memorandum)
Figure 3-1. Flowchart of the 3-day biological assessment program evaluation process.
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The Biological Assessment Program Review February 2013
During the first part of the reviewthe overviewthe reviewer leads the team in a discussion
of the water quality agency's monitoring and assessment program, WQS and programs such as
the Total Maximum Daily Load (TMDL), National Pollutant Discharge Elimination System
(NPDES) permits, and nonpoint source programs. The discussion also serves as baseline fact
finding for scoring each of the 13 technical elements of a biological assessment program and for
identifying how the agency is currently using biological assessments and considering future
applications (a complete listing of all annotated discussion topics is available in Appendix B:
Interview Topics for Agency Review). This discussion provides managers and technical
personnel with a better understanding of the program's history, why decisions were made, and
how managers and staff interact across the monitoring and assessment program, WQS, listing,
TMDL, NPDES, and nonpoint source programs. The discussion provides insight to the agency
participants on the current technical strengths and deficits of the biological assessment
program and the improvements needed to better support water quality management.
In the second part of the program review, the core review team evaluates 13 technical
elements of a biological assessment program associated with biological assessment design,
methods, and analysis. Through evaluation of the technical elements, the review team works
together to assign a level of rigor (1-4) for the overall program based on the factors outlined in
Chapter 2. On the basis of the discussion in the first part of the review, the review team
develops a list of recommendations that the water quality agency can use to improve its
program.
The final outcome of the program review is a technical memorandum written by the reviewer in
collaboration with the full review team. In the memorandum, the reviewer describes important
attributes of the overall program, summarizes the water quality agency's biological assessment
program, justifies the assignment of the program's level or rigor, and recommends future
actions. A step-by-step guide for conducting a biological assessment program evaluation is
below.
3.2 Preparation for the Review
For a biological program review to be successful, preparation is necessary for the reviewer as
well as the water quality agency personnel. Key tasks for the water quality agency include
1) identifying a comprehensive list of program managers and staff to attend the review;
2) communicating the importance and purpose of each person's participation; and 3) providing
materials that the expert reviewer uses to become knowledgeable about the state program.
3.2.1 Identifying Participants
It is essential that water quality agency personnel from different program areas are engaged in
the discussions so that data quality and information requirements are accurately represented
and properly implemented, especially with regard to EPA published methodologies.
Participation from different water quality programs, for example, is also important in the
review to build a shared understanding and broad perspective on the existing use of biological
assessment information and to begin to identify the technical program gaps and areas for
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The Biological Assessment Program Review February 2013
improved use. One person from the water quality agency is designated as the lead for the
effort. This state contact is responsible for bringing together the appropriate state personnel
and ensuring that necessary documentation is compiled for the review.
Participants should include both agency managers and staff involved in the following programs:
WQS
Monitoring and assessment
Reporting and listing
- Section 305(b)/303(d) integrated report and listings
TMDL development and implementation
Planning
Nonpoint source assessment and management
Dredge and fill (section 404/401)
NPDES program
Other relevant programs
The reviewer will designate a member of the water quality agency review team to serve as a
note taker. The note taker should be available for the entire evaluation and is responsible for
ensuring that all discussion is captured. These notes will aid the reviewer with developing the
technical memorandum.
3.2.2 Materials Provided as Basis for Program Review
This guidance document itself should be distributed to the water quality agency personnel prior
to beginning the program review to provide participants with an understanding of the technical
elements and the checklist process. The document also introduces the water quality agency to
the next steps in the biological criteria implementation process, including the option for the
water quality agency to develop a timeline for achieving a biological assessment program of
Level 4 rigor by setting specific milestones for program development.
The appendices include the materials to be used during the evaluation and as supplemental
information. By reviewing this chapter and appendices prior to the on-site visit, personnel can
familiarize themselves with their content. Some of these documents serve simply as templates
and are modified by the reviewer prior to the review.
Agenda (Appendix A)outlines the basic structure of a biological assessment program
evaluation. It is conceptual in design, open to input from both the water quality agency
and reviewer, and serves as a starting point for coordinators to plan the evaluation. A
review-specific agenda is developed prior to the review itself.
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The Biological Assessment Program Review February 2013
Water Quality Agency Interview Topics (Appendix B)provides an overview of the
major topics addressed during the biological assessment evaluation. The water quality
agency is also encouraged to identify topic areas of interest and is free to steer the
discussion accordingly. The reviewer and note taker each utilize this format for
recording answers and discussion content.
Water Quality Agency Self-Assessments (Appendix C)designed to facilitate internal
consideration about how the water quality agency's present biological assessment
program can respond to specific water quality program information needs.
Technical Memorandum Template (Appendix D)serves as an example of the scope
and content of the technical memorandum, the principal product of the biological
assessment program evaluation.
Technical Elements Checklist (Appendix E)worksheet for evaluating the degree of
development for each technical element of an agency's biological assessment program
and associated comments on the elements for the biological assessment program.
3.2.3 Preparation of Documents
Prior to the review, the water quality agency compiles documentation that describes the state's
decision-making process, the legal and regulatory framework, and technical components of the
overall water quality management program (electronic links or documents are preferred).
Access to the following materials should be provided to the independent expert reviewer prior
to the site visit:
Monitoring strategy
WQS documents
Biological standard operating procedures (SOPs)
Listing methodology/guidance
Section 305(b) report/303(d) list
Example biological assessment reports/watershed assessments
Any other materials the agency might determine relevant to the review, such as SOPs
for other types of data (e.g., stressors, Geographic Information Systems [GIS])
The reviewer uses these materials to prepare for the interview and in developing the technical
memorandum. The water quality agency also prepares an overview of its biological program
that includes a brief history and a description of both current and planned program
developments. The detail and mode of this presentation is left to the discretion of the water
quality agency.
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The Biological Assessment Program Review February 2013
3.3 Part 1: Overview of Current Water Quality Program
3.3.1 Introduction and Overviews
(1) Participants
At the beginning of the evaluation, the water quality agency lead introduces managers and
technical staff and briefly describes the purpose and scope of the biological assessment
program review process. Individual personnel also offer detail about their specific roles with
respect to the water quality agency's biological assessment program. The introductions provide
an opportunity for the reviewer to become more familiar with the participants.
(2) Role of Biological Assessment
The reviewer begins the evaluation by giving a presentation to briefly introduce the key
concepts of biological assessment-based aquatic life uses and biological criteria in relation to a
water quality agency's biological monitoring and assessment program. The presentation,
Aquatic Life Uses: A Conceptual and Practical Basis for Determining Water Quality Management
Goals and Outcomes Using Biological Assessments, covers the relationships of biological,
chemical, and physical indicators and criteria in the assessment of a water body's ecological
health and the importance of using a system with which the biological response to stress in a
water body can be evaluated. Topics included are:
The linkage of biological assessments to other monitoring and assessment programs,
with a focus on the WQS program.
Information on how a biological assessment-based approach to water quality
management support meeting the goals set forth by the water quality agency and Clean
Water Act (CWA).
Case examples of biological assessment programs that either currently achieve, or are
building towards, high quality technical programs.
(3) Agency Objectives for Biological Assessment
The next step of the process is the water quality agency presenting an overview of its biological
assessment program. This overview helps inform the assessment of the technical elements that
follows by defining current technical components, use of the biological assessment information,
and how the information produced aligns with managers' expectations and information needs.
The water quality agency monitoring coordinator is asked to articulate how the water quality
agency views the purpose, goals, and objectives of its monitoring program. This is helpful to
have on record as it defines, in the water quality agency's own words, what the water quality
agency wants to accomplish and how it intends to use information gathered from monitoring
efforts. The water quality agency should include a brief history and any current developments
or updates, but the remainder of the presentation's specifics is left up to the water quality
agency. Personnel can develop an overview that is water quality agency- and program-specific
by highlighting the key aspects that are self-identified as being of high importance.
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3.3.2 Monitoring and Assessment
Monitoring and assessment includes the systematic collection of data from the environment
and their subsequent analysis to allow assessments regarding attainment status, severity, and
extent of impairments, stressor identification, and pollutant source identification. Monitoring
and assessment is used to support the reporting requirements mandated by the CWA and other
water quality agency efforts to characterize the status of water bodies and plan and implement
restoration efforts. Discussion of current agency data quality objectives and measurement
quality objectives (DQOs and MQOs, respectively) is a critical part of this discussion and
documentation. In addition to specific agency objectives, it is useful to gather information on
whether the agency aligns its monitoring program with, or directly feeds into, local and federal
monitoring and assessments. When the agency personnel later conduct a self-assessment, the
DQOs, MQOs, and other information will factor into this assessment and might be reviewed
and revised as a consequence.
The following information is discussed during the evaluation:
Spatial sampling designThe water quality program personnel describe the sampling
design(s) employed by the water quality agency (e.g., how the water quality agency
determines sampling locations, such as using a rotating basin approach, a probability-
based approach, or via fixed stations). In addition, the water quality agency identifies
the various water body types for which a monitoring and assessment program exists, as
the design might vary among resource types.
Index periodsThe water quality agency clarifies whether a seasonal index period exists
by indicator and/or assemblage and whether considerations are given for index periods
during attenuated flows.
Chemical/physical/whole effluent toxicity (WET) assessmentTo clarify the design and
logistics of the water quality agency's sampling regime (e.g., chemical, physical, WET),
the agency personnel provide the reviewer with specifics regarding survey design,
parameters and indicators, sampling frequency, sampled media (i.e., water, sediment,
fish tissue), and the type of samples collected (e.g., grabs, composites). In addition, the
group identifies goals of the sampling, such as characterizing ambient conditions, long-
term trend assessments, and the determination of reference conditions. Finally, agency
personnel provide the reviewer with information regarding laboratory support,
specifically quality assurance/quality control (QA/QC) procedures and analytical costs.
Reference conditionAgency personnel provide information on whether reference sites
have been established, and if so, how many and for what period. The water quality
agency provides additional detail about reference conditions, such as how reference is
determined (e.g., reference site selection), and explanation of the spatial organization of
reference sites and the degree to which these sites are stratified by landscape or other
classification schemes and method for determining nonattainment of reference
condition (i.e., membership or non-membership in a set of reference sites).
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Data processing and managementA relational database is essential to a highly
rigorous biological assessment program. The water quality agency provides information
on several technical elements related to data: (1) how biological, chemical, and physical
data are stored and whether analysis can be conducted across multiple sampling types
and data sets; (2) data management QA/QC procedures (including any documentation);
and (3) the accessibility of these data to both agency personnel and outside parties.
Basin assessmentsThe water quality agency responds to questions about the scale of
basin assessments (e.g., using hydrologic unit code [HUC] units as a basis for expressing
spatial scale), how basins are selected, the number of sites in a typical assessment unit
(e.g., site density), and the number of basin assessments the water quality agency
conducts each year. In addition, any stratifying factors are discussed, such as watershed
area or stream order, flow, and the total number of sampling sites. Analysis of the data
acquisition process culminates with a discussion of the study planning process to
determine the level of integration, if any, of the various monitoring disciplines and
interactions with water quality management programs. Finally, to garner an
understanding of the assessment process, the sequence of data analysis and reporting
will be determined and any logistical concerns identified.
Monitoring strategyThe water quality agency provides the latest version of its
monitoring strategy for review and responds to questions about the frequency of
updates. Through discussion the reviewer will establish whether DQOs are clearly
defined and evaluate the usefulness of the strategy to guide implementation of the
monitoring program and to ensure use of the information to support water quality
program information needs.
ResourcesThe water quality agency provides specifics regarding the allocation of full
time employees (FTEs), particularly how they are allocated to monitoring and
assessment for each of the major scientific disciplines and the proportion of monitoring
and assessment FTEs compared to those devoted to other water quality management
programs. The water quality agency should provide an organizational table for the CWA
components of the various programs at the staff level, and it should include any
contracted resources. Finally, the water quality agency should identify current funding
sources, any existing resource limitations, and what additional resources, if any, are
needed.
3.3.3 Reporting and Listing (CWA sections 305[b] and 303[d]) and TMDLs
This part of the evaluation deals with the process of producing integrated CWA section 305(b)
and 303(d) reports, which identify waters with impaired or threatened uses, and TMDLs. These
reports are often used to delineate program priorities and allocate resources, and the
information in these reports will help the reviewer make determinations about how its
biological assessment program is used.
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Identification of waters with impaired or threatened usesThe water quality agency
provides information on the procedures, protocols, and assessment methods for
identifying waters with impaired or threatened uses. The water quality agency provides
details on what data (biological, physical, and/or chemical) and methodology are used
to determine aquatic life use impairments, and whether such impairments are based on
assessment of aquatic life assemblages. Discussion can include the degree to which
impairments are characterized for level of severity, extent, and cause. Finally, the water
quality agency provides details on the extent to which the state's waters have been
assessed and what percentage of the total waters this figure comprises.
Data acquisition and management processThe water quality agency explains the
process for making assessments of condition and status, including how the data and
information is documented and quality controlled and protected against unauthorized
changes. The water quality agency also describes requirements regarding any data
acquired by outside organizations (e.g., volunteer groups, water collaboratives), such as
admission requirements and accuracy determinations. Finally, the reviewer evaluates
the water quality agency's legislation (if any) pertaining to data management.
CWA section 303(d) list topicsThe water quality agency should describe the extent to
which biological assessment information has been used to identify waters with impaired
or threatened uses, under which 305(b)/303(d) integrated reporting categories such
waters are assigned, and how the information is used in the planning process for
establishing TMDL development schedules as part of the 303(d) list submittal. The water
quality agency should also describe and discuss any issues concerning the integration of
biological information into one assessment methodology for both CWA section 305(b)
and 303(d) reporting.
CWA section 303(d) list and TMDL development and implementation topicsThe water
quality agency should describe the extent to which data from biological assessments
and stressor identification evaluations are used in the development of TMDLs and the
evaluation of their implementation. Finally, the reviewer will want to discuss any
specific CWA section 303(d) or TMDL resource considerations.
3.3.4 Water Quality Standards
The WQS section of the review focuses on the development and integration of designated
aquatic life uses and biological criteria in the state's WQS program. WQS are the basis for
judging the effectiveness of water quality management programs. The water quality agency
should provide all participants with a copy of the state's WQS during the evaluation, and the
reviewer asks participants to refer to specific parts of the document as they become relevant
during the discussion.
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General issuesThe water quality agency describes the basis of the agency's WQS, such
as how chemical water quality criteria are derived and whether site-specific criteria
have ever been developed. The water quality agency describes its antidegradation
policy and implementation procedures. The discussion should also include how the
monitoring and assessment program is integrated with the WQS program.
Designated usesThe water quality agency should provide a description of its aquatic
life use designations and explain the process for assigning uses to water bodies. The
reviewer will want the agency to describe any other special considerations, such as
tributary rules and application of default uses. In addition, any triggers for re-
designations should be described. The water quality agency should describe what it
recognizes as waters meeting the CWA section 101(a)(2) goals.
Use attainability analysis (UAA)The water quality agency should explain its protocol
for conducting a UAA and describe what data or information might initiate the process.
Discussion of current technical issues or obstacles encountered when conducting UAAs
can be included to help determine need for additional biological assessment
information or other types of environmental data.
Biological criteriaThe water quality agency provides the reviewer with information to
determine whether biological criteria have been developed and whether such criteria
are narrative, numeric, or both. Secondly, participants describe habitat assessments and
associated criteria, if applicable. The agency provides information to help the reviewer
understand the linkage between biological criteria and aquatic life designated uses and
how this information has been used to support water quality management programs.
3.3.5 Integration of Monitoring, Reporting, Standards, and Management
Integrating information gathered from monitoring and assessment efforts with other water
quality management programs is integral to the overall program's effectiveness. The topics
below are designed to assess the state's development, use, and integration of biological
assessment information into water quality management programs.
Indicators for surface watersThe water quality agency should describe its existing
measures of the effectiveness of its water quality management programs. In addition,
the agency should gauge the dependency of these indicators on monitoring data and
identify the most important measures of water quality management program success.
Program integrationThe water quality agency explains how water quality
management programs have relied on information gathered from ambient monitoring
and assessment, focusing discussion on specific programs, including WQS, nonpoint
source assessment and management, TMDLs, NPDES permitting, CWA section 404/401
dredge and fill permits, and any other important permitting and planning schemes. The
agency should explain how data gathered via monitoring and assessments are viewed in
context of their importance to application to other water quality management
programs.
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TrainingThe water quality agency provides information on training of agency program
personnel, including the depth of training and its frequency. In addition, the water
quality agency clarifies whether such training is extended to outside entities affected by
management programs.
3.3.6 Self-Assessments
During the on-site review, the water quality agency completes two self-assessments. In the self-
assessments, the reviewer guides the water quality agency through discussion questions (see
Appendix C) to discuss how its existing program would respond to given situations and to
consider what additional technical capability would optimize its program capability and
efficiency. Cross program discussion will foster a more complete understanding within the
agency of whether the current biological assessment program is providing the needed data and
information in the appropriate time frame to support multiple water quality programs and
potentially identify areas where technical changes would enhance use of the data and better
support agency water quality program goals and objectives.
The water quality agency is asked to modify the discussion questions prior to the on-site
evaluation to make them as relevant and applicable as possible, including substituting any
terminology (e.g., specific types of aquatic resources). Agency personnel proceed through each
of the discussion questions and summarize how the programs currently incorporate biological
assessment information to support their programs and develop recommendations for
improvements. Agency personnel are encouraged to include comments describing each answer
and specifics on how the current state program would respond to the discussion question.
Upon completion, the reviewer collects the information and recommends and uses them to
help develop recommendations for technical development of the biological assessment
program to be included in the technical memorandum.
3.4 Part 2: Technical Elements Evaluation
Following a brief presentation regarding the technical elements evaluation process, the
reviewer leads a discussion about the 13 technical elements (described in chapter 2). During
this discussion participants provide input on scoring (see chapter 2 and Appendix E). Once a
score has been assigned for each of the 13 elements, the numbers are tabulated and converted
to a percentage that yields the agency's level of rigor. The water quality agency also provides
information about any in-progress improvements to the biological assessment program that
will result in the elevation of the score for specific technical elements.
3.4.1 Technical Elements of State Biological Assessment Programs: A Process to
Evaluate Program Rigor and Comparability
The review typically begins with an overview presentation of the evaluation process. The
presentation can include ways states and tribes can determine their current level of rigor and
how to use this information to achieve specific milestones to improve the overall level of
program rigor. The overview can also include examples of previous assessments, specifically
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those from the EPA regional pilots that were conducted annually during 2002-2008 (Yoder and
Barbour 2009; this document). The presentation might also include general recommendations
that were made to the pilot states and tribes, which prescribe implementing high-level
biological assessment programs as a continual, iterative process involving the creation of
regional working groups consisting of water quality agency staff and regional EPA personnel.
3.4.2 Technical Elements Checklist
As described in Chapter 2, the 13 technical elements checklist (see Appendix E) is used to assign
a level of rigor to a water quality agency's biological assessment program. Agency personnel
and the reviewer will discuss the basis for the scores using the checklist for each of the 13
elements. The reviewer will assign a preliminary score for each of the 13 elements and take
notes regarding the score's justification and any ongoing water quality agency efforts and/or
program developments that would affect the score. A tour of field and/or laboratory facilities
might also be conducted during this portion of the review. Once each of the 13 elements has
been scored, the results are tabulated and a score is assigned. These results are discussed by
the review team and steps to address program gaps are identified. The score determines the
level of rigor of an agency's biological assessment program. The water quality agency and
reviewer will discuss the results of the technical elements exercise during the on-site visit and
through follow-up conversations after the technical memorandum has been received and
reviewed by the water quality agency.
3.5 Preparation of Technical Memorandum
The final output of the biological assessment program evaluation is the technical
memorandum. Using the detailed information and documents provided by the water quality
agency, the reviewer prepares a technical memorandum that summarizes the agency's
biological assessment program, assigns the program a level of rigor, and justifies this
assignment by providing the scoring's rationale. The technical memorandum includes
recommendations on how the water quality agency can improve its biological assessment
program and the development and use of numeric biological criteria, and on what steps it can
take to achieve a higher level of rigor. These recommendations typically include enhancements
relative to design, methodology, and execution of credible data.
Following completion of the technical memorandum, the reviewer submits it to the water
quality agency and EPA regional staff for review and comment. Once the comments are
received, they are incorporated into a final version. A template for the technical memorandum
is available in Appendix D.
3.6 Action Plan Development
The ultimate goal of the biological program review is to produce the data and information
needed by water quality agencies to strategically plan and allocate resources to develop and
support a high-quality biological assessment program. In addition to evaluating the technical
elements of a biological assessment program, identification of water quality program
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information needs (e.g., CWA section 303[d] listing, TMDLS, NPDES, nonpoint sources) and the
flow of data from the monitoring program to the different water quality programs is an
essential part of the evaluation. The program review produces technical recommendations for
development of a high-quality biological assessment program and for effective use of the data
and information that the technical program will generate.
In 2006 EPA Region 5 convened a region and state workshop on development of biological
assessment and criteria programs. A central theme at the workshop was the importance of
parallel efforts to:
Establish early dialogue between management and technical staff to determine how
high quality biological assessment information will be incorporated into the water
management program. This dialogue is critical to ensure that the monitoring program
plans for the design and production of data and information that will support water
program information needs.
Plan for the appropriate use of biological assessment information as the monitoring and
assessment program's level of technical rigor increases. At all levels of technical
development, biological assessment information can be used to support water quality
decisions. The degree of confidence with which this can be done varies depending on
the questions being addressed. The information produced by a program with a low level
of rigor might be used to support screening for high-quality or severely degraded
conditions (e.g., looking for "hot spots" that need immediate attention) and to identify
water quality limited waters. Additionally, the biological assessment methods
characteristic of a low level program might be used to support special studies as long as
the degree of confidence (e.g., within site variability) is characterized and documented.
As the level of program rigor is increased, more comprehensive and detailed condition
assessments can be produced to further support CWA section 305(b) reporting and
303(d) listing decisions and report environmental outcomes from water quality
management actions. As the state further develops and refines its biological assessment
measures in conjunction with chemical, physical, WET, and landscape assessments, the
monitoring and assessment program is increasingly able to provide information that
contributes to stressor identification and development of attainable restoration targets.
Based on the discussions with the 23 program reviews done to date, the technical program
needs to be developed within context of management needs and agency policy so that the
information ultimately produced is used to support water quality management. For example, a
biological assessment program with a high level of rigor might have the technical capability to
develop biological measures sensitive to early changes in biological assemblages. The agency
might consider incorporating these measures into its numeric biological criteria and refining its
aquatic life uses to support protection of excellent and good conditions and implement
preventive actions. In the pilot states where the dialogue between the monitoring program and
the parts of the water program that use the data did not occur regularly, biological assessment
information to support water quality management had not been fully realized.
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3.7 Summary
The integration of rigorous biological assessments with other environmental data and
assessments (e.g., chemical, WET, physical, landscape) is important for developing a
comprehensive, data-driven but cost effective approach to support water quality management
(USEPA 2011c). Despite advancements and successes in water quality management since the
CWA was enacted, pollutants (e.g., pathogens, metals, nitrogen, and phosphorus pollution)
continue to be major causes of water quality degradation. Additionally, the impact of other
significant stressors, including habitat loss and fragmentation, hydrologic alteration, invasive
species, and climate change, can be better understood using analytical tools and information
that can operate at the ecosystem scale, such as biological assessments.
The biological assessment program review can be a first step toward identifying the specific
actions a water quality agency can take to attain a rigorous biological assessment program.
Additionally, an agency's overall ability to make management decisions is enhanced by using
biological assessment to more precisely define designated aquatic life uses, develop numeric
biological criteria, and associate biological response to chemical, physical, and landscape data
(USEPA 2011c). The results of the review are intended to inform incremental technical
development, future use refinements, and biological criteria derivation in context of sound
scientific information and well-integrated monitoring and assessment information. For
example, Minnesota's biological assessment program underwent a review in 2005 and then
developed a plan with milestones to implement the review recommendations. The review
process helped Minnesota Pollution Control Agency produce a detailed plan for technical
program development to support refining the state's designated aquatic life uses and
development of numeric biological criteria for streams and rivers.8 Likewise, the California
biological assessment program underwent a technical elements review in 2009. At the time of
the review, California was already implementing a plan to develop its biological assessment
program, but participation in the review process helped California align its program to the
national elements framework. This helped California reinforce the importance of several key
program elements (e.g., reference conditions, data management) and helped secure sustained
management support. In 2009 the state initiated a public process to develop biological
objectives (numeric biological criteria) for perennial streams and rivers.9 This effort has
included the development of guidance for selecting and evaluating candidate causes of
biological impairment in different regions of the state, using the EPA's causal assessment
process as a starting point. The biological objectives will be used to establish numeric scoring
tools for measuring stream ecological integrity and define numeric thresholds needed to
protect the state's designated aquatic life uses.
Aquatic life can vary from water body to water body. One major challenge in defining and
assessing designated aquatic life uses is separating the natural variability that is a function of
water body type and the ecological region from the variability that results from exposure to
8http://www.pca.state.mn.us/index.php/water/water-permits-and-rules/water-rulemaking/tiered-aquatic-life-
use-talu-framework.html
9 http://www.waterboards.ca.gov/plans_policies/biological_objective.shtml
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stressors. Rigorous biological assessment programs can provide the detailed information
required to more precisely define the expected biotic community for a water body and derive
numeric biological criteria. By accounting for natural variability in aquatic systems, rigorous
biological assessments can help reduce a source of uncertainty and error in water quality
management. Additionally, in nature there is a continuous gradient of biological response to
increasing exposure to stressors. A rigorous biological assessment program can support other
agency water quality programs with the technical capability to discriminate levels of biological
response along a stressor gradient to help identify and protect high-quality waters and set
attainable restoration goals for degraded waters.
By conducting rigorous biological assessments in conjunction with chemical, WET, physical, and
landscape data and assessments, more detailed relationships between the aquatic resource,
stressor agents, and management actions can be developed. This means that an agency's
biological assessment program can provide data and information for more than general status
assessments as required by CWA section 305(b) and that can be used to inform impact
assessments, studies, and investigations to support an agency's section 303(d) list, TMDL,
NPDES permitting, and nonpoint source programs. Each of these programs relies on monitoring
and assessment and the WQS programs to provide an accurate delineation of impairments and
their associated causes, as well as determine attainment of specific requirements (e.g., criteria)
on which calculations of water quality based limits are based.
The biological assessment program review process provides information and technical
recommendations to the agency to further develop its technical rigor and to enhance program
application. It is the agency's decision on when and how to implement the review results and
recommendations for program improvements. Involvement of EPA staff in the review process is
recommended to align agency efforts and resources to support the desired program
development and foster agency partnerships. For example, regional EPA staff was involved
throughout the Minnesota review and were instrumental is aligning EPA support and
assistance. In California, strong and sustained support from regional EPA staff helped
consolidate the state's biological assessment infrastructure development and enabled the state
to rapidly develop the technical basis for the state's biological criteria. If an agency is interested
in conducting a biological assessment program review, it is recommended that agency
personnel contact EPA's regional or headquarters biological criteria program for further
information and to plan a review.
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Acronyms
BCG
BMP
BPJ
CALM
CWA
DELT
DQO
EOLP
EPA
EPT
FTE
CIS
HELP
HUC
IBI
IT
MDEP
MQO
NPDES
NYSDEC
Ohio EPA
QA
QC
PAH
and Abbreviations
biological condition gradient
best management practice
best professional judgment
Consolidated Assessment and Listing Methodology
Clean Water Act
deformities, erosions, lesions, and tumors
data quality objective
Erie Ontario Lake Plain
U.S. Environmental Protection Agency
ephemeroptera, plecoptera, trichoptera taxa
full-time employee
geographic information system
Lake Huron/Lake Erie Plain
hydrologic unit code
index of biological/biotic integrity
information technology
Maine Department of Environmental Protection
measurement quality objective
National Pollutant Discharge Elimination System
New York State Department of Environmental Conservation
Ohio Environmental Protection Agency
quality assurance
quality control
polycyclic aromatic hydrocarbon
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RDBMS relational database management system
SOP standard operating procedure
TMDL total maximum daily load
UAA use attainability analysis
WET whole effluent toxicity
WQS water quality standards
WSA Wadeable streams assessment
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GLOSSARY
aquatic assemblage
aquatic community
aquatic life use
attribute
benthic macroinvertebrates or
benthos
best management practice
biological assessment or
bioassessment
biological criteria or biocriteria
biological indicator or bioindicator
biological integrity
An association of interacting populations of organisms in a
water body; for example, fish assemblage or a benthic
macroinvertebrate assemblage.
An association of interacting assemblages in a water body, the
biotic component of an ecosystem.
A beneficial use designation in which the water body provides,
for example, suitable habitat for survival and reproduction of
desirable fish, shellfish, and other aquatic organisms.
The measurable part or process of a biological system.
Animals without backbones, living in or on the sediments, of a
size large enough to be seen by the unaided eye and which can
be retained by a U.S. Standard no. 30 sieve (28 meshes per
inch, 0.595-mm openings); also referred to as benthos,
infauna, or macrobenthos.
An engineered structure or management activity, or
combination of those, that eliminates or reduces an adverse
environmental effect of a pollutant.
An evaluation of the biological condition of a water body using
surveys of the structure and function of a community of
resident biota.
Narrative expressions or numeric values of the biological
characteristics of aquatic communities based on appropriate
reference conditions; as such, biological criteria serve as an
index of aquatic community health.
An organism, species, assemblage, or community characteristic
of a particular habitat, or indicative of a particular set of
environmental conditions.
The ability of an aquatic ecosystem to support and maintain a
balanced, adaptive community of organisms having a species
composition, diversity, and functional organization comparable
to that of natural habitats in a region.
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biological monitoring or
biomonitoring
biological survey or biosurvey
Clean Water Act
Clean Water Act 303(d)
Clean Water Act 305(b)
criteria
DELT
designated uses
disturbance
ecoregion
Use of a biological entity as a detector and its response as a
measure to determine environmental conditions; ambient
biological surveys and toxicity tests are common biological
monitoring methods.
Collecting, processing, and analyzing a representative portion
of the resident aquatic community to determine its structural
and/or functional characteristics.
The act passed by the U.S. Congress to control water pollution
(formally referred to as the Federal Water Pollution Control Act
of 1972). Public Law 92-500, as amended. 33 U.S.C. 1251 et
seq.
This section of the act requires states, territories, and
authorized tribes to develop lists of impaired waters for which
applicable WQS are not being met, even after point sources of
pollution have installed the minimum required levels of
pollution control technology. The law requires that the
jurisdictions establish priority rankings for waters on the lists
and develop TMDLs for the waters. States, territories, and
authorized tribes are to submit their lists of waters on April 1 in
every even-numbered year.
Biennial reporting requires description of the quality of the
nation's surface waters, evaluation of progress made in
maintaining and restoring water quality, and description of the
extent of remaining problems.
Elements of state water quality standards, expressed as
constituent concentrations, levels, or narrative statements,
representing a quality of water that supports a particular use.
When criteria are met, water quality will generally protect the
designated use.
Presence of deformities, erosions, lesions, and tumors as a
measure of organism health, typically assessed for fish.
Those uses specified in WQS for each water body or segment
whether or not they are being attained.
Human activity that alters the natural state and can occur at or
across many spatial and temporal scales.
A relatively homogeneous ecological area defined by similarity
of climate, landform, soil, potential natural vegetation,
hydrology, or other ecologically relevant variables.
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function
guild
historical data
index of biological/biotic integrity
invasive species
least disturbed condition
metric
minimally disturbed condition
multimetric index
Processes required for normal performance of a biological
system (might be applied to any level of biological
organization).
A group of organisms that exhibit similar habitat requirements
and that respond in a similar way to changes in their
environment.
Data sets from previous studies, which can range from
handwritten field notes to published journal articles.
An integrative expression of site condition across multiple
metrics; an IBI is often composed of at least seven metrics.
A species whose presence in the environment causes economic
or environmental harm or harm to human health. Native
species or nonnative species can show invasive traits, although
that is rare for native species and relatively common for
nonnative species. (Note that this term is not included in the
biological condition gradient [BCG].)
The best available existing conditions with regard to physical,
chemical, and biological characteristics or attributes of a water
body within a class or region. Such waters have the least
amount of human disturbance in comparison to others in the
water body class, region, or basin. Least disturbed conditions
can be readily found but can depart significantly from natural,
undisturbed conditions or minimally disturbed conditions.
Least disturbed condition can change significantly over time as
human disturbances change.
A calculated term or enumeration that represents some aspect
of biological assemblage, function, or other measurable aspect
and is a characteristic of the biota that changes in some
predictable way with increased human influence.
The physical, chemical, and biological conditions of a water
body with very limited, or minimal, human disturbance.
An index that combines indicators, or metrics, into a single
index value. Each metric is tested and calibrated to a scale and
transformed into a unitless score before being aggregated into
a multimetric index. Both the index and metrics are useful in
assessing and diagnosing ecological condition. See index of
biological/biotic integrity.
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narrative biological criteria
native
nonnative or intentionally
introduced species
Written statements describing the structure and function of
aquatic communities in a water body that support a designated
aquatic life use.
An original or indigenous inhabitant of a region; naturally
present.
With respect to an ecosystem, any species that is not found in
that ecosystem; species introduced or spread from one region
of the United States to another outside their normal range are
nonnative or non-indigenous, as are species introduced from
other continents.
numeric biological criteria
periphyton
rapid bioassessment protocols
reference condition (biological
integrity)
Specific quantitative measures of the structure and function of
aquatic communities in a water body necessary to protect a
designated aquatic life use.
A broad organismal assemblage composed of attached algae,
bacteria, their secretions, associated detritus, and various
species of microinvertebrates.
Cost-effective techniques used to survey and evaluate the
aquatic community to detect aquatic life impairments and their
relative severity.
The condition that approximates natural, unaffected conditions
(biological, chemical, physical, and such) for a water body.
Reference condition (biological integrity) is best determined by
collecting measurements at a number of sites in a similar water
body class or region undisturbed by human activity, if they
exist. Because undisturbed conditions can be difficult or
impossible to find, minimally or least disturbed conditions,
combined with historical information, models, or other
methods can be used to approximate reference condition as
long as the departure from natural or ideal is understood.
Reference condition is used as a benchmark to determine how
much other water bodies depart from this condition because of
human disturbance.
See minimally disturbed condition and least disturbed
condition
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reference site
sensitive taxa
sensitive or regionally endemic
taxa
A site selected for comparison with sites being assessed. The
type of site selected and the types of comparative measures
used will vary with the purpose of the comparisons. For the
purposes of assessing the ecological condition of sites, a
reference site is a specific locality on a water body that is
undisturbed or minimally disturbed and is representative of
the expected ecological integrity of other localities on the same
water body or nearby water bodies.
Taxa intolerant to a given anthropogenic stress; first species
affected by the specific stressor to which they are sensitive and
the last to recover following restoration.
Taxa with restricted, geographically isolated distribution
patterns (occurring only in a locale as opposed to a region),
often because of unique life history requirements. Can be long-
lived, late-maturing, low-fecundity, limited-mobility, or require
mutualist relation with other species. Can be among listed
endangered/threatened or special concern species.
Predictability of occurrence often low; therefore, requires
documented observation. Recorded occurrence can be highly
dependent on sample methods, site selection, and level of
effort.
sensitive - rare taxa
sensitive - ubiquitous taxa
Taxa that naturally occur in low numbers relative to total
population density but can make up large relative proportion
of richness. Can be ubiquitous in occurrence or can be
restricted to certain microhabitats, but because of low density,
recorded occurrence is dependent on sample effort. Often
stenothermic (having a narrow range of thermal tolerance) or
coldwater obligates; commonly k-strategists (populations
maintained at a fairly constant level; slower development;
longer lifespan). Can have specialized food resource needs or
feeding strategies. Generally intolerant to significant alteration
of the physical or chemical environment; are often the first
taxa observed to be lost from a community.
Taxa ordinarily common and abundant in natural communities
when conventional sample methods are used. Often having a
broader range of thermal tolerance than sensitive or rare taxa.
These are taxa that constitute a substantial portion of natural
communities and that often exhibit negative response (loss of
population, richness) at mild pollution loads or habitat
alteration.
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stressors
structure
taxa
taxa of intermediate tolerance
Physical, chemical, and biological factors that adversely affect
aquatic organisms.
Taxonomic and quantitative attributes of an assemblage or
community, including species richness and relative abundance
structurally and functionally redundant attributes of the
system and characteristics, qualities, or processes that are
represented or performed by more than one entity in a
biological system.
A grouping of organisms given a formal taxonomic name such
as species, genus, family, and the like.
Taxa that compose a substantial portion of natural
communities; can be r-strategists (early colonizers with rapid
turnover times; boom/bust population characteristics). Can be
eurythermal (having a broad thermal tolerance range). Can
have generalist or facultative feeding strategies enabling use of
relatively more diversified food types. Readily collected with
conventional sample methods. Can increase in number in
waters with moderately increased organic resources and
reduced competition but are intolerant of excessive pollution
loads or habitat alteration.
threatened waters
tolerant taxa
total maximum daily load
water quality management
(nonregulatory)
Waters that are currently attaining water quality standards,
but which are expected to exceed water quality standards by
the next 303(d) listing cycle.
Taxa that compose a small proportion of natural communities.
They are often tolerant of a broader range of environmental
conditions and are thus resistant to a variety of pollution- or
habitat-induced stresses. They can increase in number
(sometimes greatly) in the absence of competition. Commonly
r-strategists (early colonizers with rapid turnover times;
boom/bust population characteristics), able to capitalize when
stress conditions occur; last survivors.
The calculated maximum amount of a pollutant a water body
can receive and still meet WQS and an allocation of that
amount to the pollutant's source.
Decisions on management activities relevant to a water
resource, such as problem identification, need for and
placement of best management practices, pollution abatement
actions, and effectiveness of program activity.
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water quality standard A law or regulation that consists of the designated use or uses
of a water body, the narrative or numerical water quality
criteria (including any biological criteria) that are necessary to
protect the use or uses of that water body, and an
antidegradation policy.
whole effluent toxicity The aggregate toxic effect of an aqueous sample (e.g., whole
effluent wastewater discharge) as measured by an organism's
response after exposure to the sample (e.g., lethality, impaired
growth or reproduction); WET tests replicate the total effect
and actual environmental exposure of aquatic life to toxic
pollutants in an effluent without requiring the identification of
the specific pollutants.
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APPENDIX A: AGENDA FOR ON-SITE INTERACTION MEETING
State/Tribal Agency Biological Assessment Program Evaluation
AGENDA
DAY! Date
Building # Room
9:30-10:00 am Welcome and Introductions
Refinements to the agenda
General purpose and overview
10:00-11:30 [Agency] Biological Assessment Program Review & Development
Key concepts and examples
Development of state programs
U.S. Environmental Protection Agency (EPA) methods and key
documentation
11:30-1:00 pm LUNCH
1:00-2:00 Overview of [name of water quality agency to be reviewed] Biological
Assessment Program by [Agency] staff
Brief history of [water quality agency] biological program
Current developments and updates
2:00-5:00 [Agency] Monitoring & Assessment Programfollowing list of
annotated discussion topics
Monitoring & Assessment Program
Water body types
Spatial design
Basin assessments
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Indicatorschemical, physical, biological
Data management
Resources for monitoring and assessment
Reporting & Listing
Delineation of impairments
Assessment process
305(b)/303(d)
Other program support
DAY 2 Date
Building # Room
9:00-10:30 am [Agency] Managers' Overview of Biological Assessment-based Programs
Process overview
Concepts and examples-implications for water quality standards
(WQS)
10:30-11:30 Assessment and Integration
Using indicators to measure effectiveness
Using monitoring and assessment to support water quality
management programs
11:30-1:00 pm LUNCH
1:00-3:00 Water Quality Standards
General description of [Agency] WQS
Structure of designated uses and attendant criteria
Aquatic life uses and biological criteria
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Use attainability analyses (UAAs), site-specific modifications, etc.
Implications
3:00-5:00 Agency Self-Assessments
Complete agency self-assessments and discuss results (might be
beneficial to have the agency complete the self-assessments prior
to the biological assessment program evaluation)
DAY 3 Date
Building # Room
8:30-11:30 am Technical Elements Review of [Agency] Biological assessment Program
Overview of technical elements review process
Scoring each element in the technical elements checklist
11:30-1:00 pm LUNCH
1:00-2:00 Technical Elements Review (continued)
2:00-4:30 Q&A
Follow-up on any of the previous days' topics
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APPENDIX B: INTERVIEW TOPICS FOR AGENCY REVIEW
State/Tribal Monitoring and Assessment and Water Quality Standards Program Interviews:
Annotated List of Discussion Topics
Introduction
A critical component of the biological program review is the detailed interviews of key agency
program managers and staff. The purpose of these discussions is to understand the existence
and extent of data-driven water quality management. These interviews are an opportunity to
better define and understand the uses of monitoring and assessment information in the water
quality agency and to determine the opportunities, incentives, impediments, and barriers to the
fuller use of this information in support of water quality management programs. In addition,
the interviews examine the intersections of biological assessment with water quality standards
(WQS), designated aquatic life uses, and criteria.
The biological program review is focused on current and planned uses of monitoring and
assessment information in support of all relevant water quality management programs. This
includes the following broad program areas that water quality management agencies have in
common:
WQS focusing on designated uses and criteria
Reporting and listing (watershed assessments, Clean Water Act [CWA] section
305(b)/303(d) reporting) and total maximum daily load (TMDL) development schedules
Water quality planning, TMDL development and implementation, nonpoint source
assessment and management, dredge and fill (CWA section 404/401)
National Pollutant Discharge Elimination System (NPDES) program (CWA section 402)
Managers and staff who can speak to the operation and management of these programs should
attend the interview when these topics are discussed.
The following topics are intended to guide the interview process. These topics are also intended
to help the agency determine who from the agency programs should attend each day's
discussions.
Monitoring and Assessment Program
Monitoring is the systematic collection of chemical, physical, and biological (including WET)
data in the ambient environment. Assessment is the analysis and transformation of that data
into meaningful information that includes attainment/nonattainment determinations,
characterization of impairments (extent and severity), associations between impaired status
and causes (i.e., agents) and sources (i.e., activity or origin), and data and information to
develop improved tools, indicators, criteria, and policies. Monitoring and assessment supports
the reporting that is required by the CWA (sections 305[b], 303[d] list, 319, etc.) and that is
used by the agency for allied purposes (watershed assessments, site-specific assessments,
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planning, TMDL development, etc.). The following are core topics for discussion. The agency
might wish to add other topics.
1. Spatial design
. Is a rotating basin approach used? Describe the sequence and cycle and, linkages to
management activities.
. Is the spatial design probability-based (scale and scope, statewide, regional, etc.)?
. Fixed station (e.g., tenure and history)
. What resource types are covered (wadeable streams, large rivers, great rivers, lakes,
wetlands, headwater streams, etc.)?
. Is the spatial design for the monitoring program aligned with, or directly feeding
into, other monitoring and assessment programs at the local, regional, or federal
level?
2. Basin assessments
. At what scale are assessments done (major basin, subbasin, watershed,
subwatershed)? Hydrologic unit code (HUC) units?
. What is the site-selection process (targeted, random, other)?
. What stratifying factors are considered (watershed area, stream order, other)?
. How many sites are assessed each year?
. What site density (i.e., the number of sites allocated to a specific study area) is
used?
. What is the data analysis and reporting sequence?
. What are the bottlenecks in data analysis and reporting?
. Are there other significant logistical issues?
. What study planning process is used? Are all affected disciplines integrated?
3. Index periods
. Describe the seasonal sampling index periods by indicator (summer-fall, monthly,
other).
. Explain the flow attenuated considerations (loading estimates, event related,
summer-fall low flow, etc.).
4. Biological (including WET)/chemical/physical assessment
. What media are assessed (water, sediment, tissues, etc.)?
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What is the purpose of sampling (ambient characterization, model calibration, long-
term trends, reference/background, etc.)?
. Which parameter groups are considered? How are the groups selected?
. What type of laboratory support is available?
. Describe the sampling design and logistics (survey design, frequency, grabs vs.
composites).
. Are there exceedance issues (magnitude, duration, frequency)?
5. Reference condition
. Have reference sites been established? For what purposes (e.g., biological criteria,
nutrients, background conditions)?
. How many reference sites are used?
. What is the spatial organization and stratification (ecoregions, hydrologic units,
physiographic regions, other)?
. How is reference condition established (data driven, cultural, least affected)?
6. Data processing and management
. How are data stored (WQX, other system)?
. How are data accessed by staff for analysis?
. What resources are dedicated to data management (full time employees [FTEs])?
. What are the quality assurance/quality control (QA/QC) procedures for ensuring
data quality?
. What is the timetable for entry and validation?
. Describe the ease of data availability within and outside the agency.
. What is the demand for data from outside the agency?
7. Monitoring strategy
. Discuss the latest monitoring strategy available (please provide a copy).
. Is the strategy a useful document?
. Should the strategy serve as documentation of data acceptability?
. Are data quality objectives (DQOs) defined?
. How frequently is the strategy updated?
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8. Resources
. How many FTEs are devoted to monitoring and assessment by discipline
(chemical/physical, biological assessment, TMDL/modeling, etc.)?
. What proportion of FTEs is devoted to water quality management programs?
(provide a table of organization for the CWA parts of the water quality agency
program)
. What funding sources are available? What are their limitations? Is the agency
leveraging resources with other programs?
. Are current resources adequate? If not, what is needed?
Reporting and Listing (305[b]/303[dJ) and TMDLs
Reporting and listing are the processes of producing the integrated CWA section 305(b)/303(d)
report, which includes the list of waters with impaired or threatened uses and TMDL
development schedules. The information contained in these reports and lists is not only
important to determining the effectiveness of a water quality agency's water quality
management programs, but is increasingly being used to set program priorities and allocate
funding. Monitoring and assessment information is an indispensable element of this process
and how it is generated and applied determines, in part, the accuracy of the statistics that are
reported and used. Thus, it is important to determine and understand how each water quality
agency uses monitoring and assessment information to support these determinations.
1. Delineation of impaired or threatened waters
. What are the procedures and protocols for determining impaired waters (including
extent and severity)?
. What are the primary arbiters of impairment and threat?
. What data qualifiers are used (analogs to the formerly used monitored and
evaluated categories)?
. What is the extent of extrapolation from single and aggregate sampling sites? How
was this developed, and has it been tested?
. What data are the basis of decisions about aquatic life use impairment (biological,
chemical/physical, mix of both, best professional judgment [BPJ], etc.)?
. Is determination of causes and sources of impairment and threat linked to an
impairment or threat?
. How are determinations of severity, extent, and incremental change made?
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How is the universe of resources defined (miles of rivers and streams, lake acres,
etc.)?
. How does the water quality agency account for the proportion of resources that are
actually assessed?
2. Assessment process
. Explain "chain-of-custody." Do the same staff who collect and analyze sampling data
also produce the assessments? Are there any "hand-offs"?
. How are data from volunteer organizations used? Are there "admission"
requirements? Any testing of accuracy? Pressure to accept data?
. How are data from other organizations handled? What are the acceptance
requirements?
. Are there requirements for credible data or similar legislation?
3. 305(b) reporting topics
. How are trends assessed (e.g., tracking of aggregate condition through time, by
resource type, designated uses, etc.)?
. How is CWA section 305(b) reporting information used by agency to guide water
quality management? Is it the 305(b) report viewed by management as a report
card? Does it have other uses? Does it distinguish impairment by point and nonpoint
sources? Any subsets within each?
. What is the extent to which outside groups use 305(b) reporting information?
. What would be the impact of any changes due to assessment method?
4. 303(d) listing and TMDLs
. Describe the relationship between former CWA section 305(b) report and existing
303(d) list (e.g., conversion process, issues, concerns, gaps, and shortfalls).
. Is TMDL development coordinated or aligned with ambient monitoring and
assessment?
. Are biological data used in the TMDL process? Are there any issues and concerns?
Conflicts?
. How are biological impairments considered? Which listing category?
. Are there sufficient biological assessment tools available to help develop defensible
TMDLs that will contribute to restoration of impaired aquatic life uses? If not, what
is needed and how long will it take?
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Water Quality Standards
WQS provide the basis for water quality management and for judging the effectiveness of
water quality management programs.
General WQS issues
. Describe the structure of the water quality agency's current WQS (designated uses,
criteria, and antidegradation policy and implementation procedures).
. How are chemical water quality criteria derived? Any modifiers or adjustment
factors?
. How are existing uses determined?
. When and where are site-specific criteria used? How many instances?
. How would better monitoring and assessment affect the WQS process?
Designated uses
. Describe aquatic life designated uses in the state WQS (a copy of the relevant parts
of the WQS is requested).
. Are individual waters designated? Are there default uses? Undesignated waters?
Tributary rules? Other issues?
. What triggers individual water body designations? Are they always downgrades?
Does anything trigger an upgrade? Is there a regular process for inventorying these
needs?
. Are there designated uses that are less than the CWA section 101(a)(2) goal uses?
Are they defined?
. Is there a process to use biological assessments to more precisely define designated
aquatic life uses and develop numeric biological criteria to protect those uses?
. What is the level of water quality agency interest in use of biological assessment to
more precisely define uses (advantages, disadvantages, barriers to development and
implementation)?
Use attainability analysis (UAA)
. Does the agency have experience with UAAs (number attempted/completed,
problems, issues)?
. Outline/describe the existing UAA process. Is it routine? Special project oriented?
What triggers a UAA? What are preferred data and information requirements?
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How do stakeholders perceive the UAA process (pros and cons, requests for and by
whom, etc.)?
. Has the emphasis on CWA section 303(d) listing increased the "interest" in UAAs?
. What criteria are used to determine attainability of uses?
. What are the likely stressors in your state? What are the sources of the stressors?
Biological criteria
. Have biological criteria been adopted or proposed (narrative, numeric)?
. How are biological criteria linked to designated uses?
. Are biological assessments used to more precisely define designated aquatic life
uses and develop numeric biological criteria?
. What are the advantages and disadvantages of biological criteria in WQS?
. How would numeric biological criteria affect the use review process?
. Describe habitat assessments and criteria.
. What are stakeholder perceptions and viewpoints on biological criteria?
Assessment Integration Issues
The integration of monitoring and assessment information within water quality management
programs is an important and emerging issue. The National Environmental Performance
Partnership System promotes joint priority setting and planning through the increased use of
environmental goals and indicators. Shared goals and milestones could be used to more
comprehensively report to the public and environmental decision makers about the status of
water resources in the water quality agency and to document progress in meeting these goals.
The goals and milestones could also be used to more effectively target programmatic efforts at
all levels. It is important to be able document achievements so that environmental successes
are recognized, funding is maintained at appropriate levels, and effective management
programs continue to be implemented. The following are aimed at assessing the water quality
agency's efforts to develop and use indicators and integrate them into water quality
management.
1. Indicators for surface waters
. What efforts have been taken to develop a process for using environmental
indicators to fulfill the role as a measure of the effectiveness of water quality
management programs (provide any documentation)?
. Are any implemented or practiced?
. How dependent are these systems on monitoring data?
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What is the awareness of past U.S. Environmental Protection Agency (EPA) indicator
development efforts (i.e., national indicators for surface waters, hierarchy of
indicators, etc.)?
. Is there any recognition of indicator roles (i.e., stress, exposure, response roles of
indicators)?
. What is (are) the most important measure(s) or indicator(s) of water quality
management program success in your water quality agency?
2. Program integration
. Are there any examples in which water quality management programs rely on
ambient monitoring and assessment information?
. Is monitoring and assessment information used to support:
o The NPDES permitting process (e.g., reasonable potential determinations and
permit compliance)? CWA section 402 NPDES program including stormwater
phase I or II?
o CWA section 319/nonpoint source planning and implementation?
o CWA 404/401 process? Other programs?
. How is monitoring and assessment information and resulting assessments and
reports, regarded by the above programs (essential, useful, nice to have,
inconsequential)?
3. Training
. Are training opportunities afforded to staff and/or management?
. How do these relate to indicators development, monitoring and assessment,
biological assessment, or ecological principles in general?
. Does your agency receive requests for field demonstrations (fish, bugs, sampling,
etc.) for internal and external purposes?
. Is training available for external entities?
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APPENDIX C: SELF-ASSESSMENTS BY STATE/TRIBAL AGENCY
MANAGERS
The self-assessment exercise is conducted during the on-site evaluation. The
technical expert walks participants through a discussion of how biological
assessment information can be more effectively used to support water quality
program needs for information. It is important that representatives from different
water quality programs participate in order to: (1) gain a cross-program
understanding of how biological assessments can be used to support multiple
water quality programs; (2) identify the type of biological assessment information
needed by their programs and timing for information delivery; and, (3) identify
efficiencies for more cost effective biological assessments. Programs interested in
conducting a review do not need to complete these self-assessment questions in
advance. The results of these discussions do not factor into scoring of the
technical elements.
The topics and questions included in the worksheets are provided as examples
that can be used to initiate cross program discussion.
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SELF-ASSESSMENT 1
Use of biological assessments to protect aquatic life use
1. Answering these questions requires a thorough understanding of the aquatic life uses in
your water quality agency's water quality standards law.
To know this, you have to be familiar with the aquatic life uses in your water quality
standards and understand what parts, if any, of the aquatic life uses are assessed
with biological assessment data.
2. For aquatic life uses that are assessed using biological assessment data, an estimate of
what biological condition gradient (BCG) level, or levels, your water quality agency's
uses provide protection is recommended;
To know this, the biological monitoring technical staff can determine (for example,
by a consensus of professional judgment) to what BCG level(s) your water quality
agency's biological criteria thresholds (e.g., numeric criteria, Rapid Bioassessment
Protocol (RBP), or Index of Biological Integrity (IBI) ranges) provide protection.
Alternatively, if your program does not have numeric biological criteria, the staff can
evaluate what BCG level your state uses for listing biologically impaired waters. In
other words, how does biologically-based aquatic life use attainment measured by
numeric biological criteria and/or CWA section 303(d)-listing thresholds map to a
BCG level?
Familiarity with your water quality agency's application of biological criteria
thresholds in regulatory decision-making is important to help identify how biological
assessment information can be used to guide the discussion on added value of
further technical improvement (i.e., be familiar with findings that have triggered an
agency response based on aquatic life use attainment as determined by biological
assessment and criteria).
Example scenarios characteristic of situations your agency encounters are
recommended to help focus the discussion and the identification of current
strengths and limitations of the biological assessment program.
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WORKSHEET FOR TOPIC 1: PROTECTION OF HIGH QUALITY WATERS
Example: A watershed with minimal impacts to aquatic systems from anthropogenic stress.
Streams, wetlands, lakes, and rivers support high quality biological communities based on
biological indices (e.g., benthic macroinvertebrates, algal, and/or fish assemblages). The
presence of reproducing native species is documented. Downstream waters such as bays and
estuaries support a range of biological conditions, including high quality biological communities
in areas that are minimally impacted.
1. Does the existing biological assessment program provide information to detect declines
in biological condition in high quality waters?
YES NO
2. If yes, does the program provide information to detect declines within the assigned
aquatic life use class?
YES NO
If no to either of the above two questions, what changes to the type, amount, or quality of
biological assessment information would be useful? Would changes to data collection and
analysis and/or internal communication contribute to the use of biological assessments? Are
there additional recommendations?
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WORKSHEET FOR TOPIC 1: PROTECTION OF HIGH QUALITY WATERS (page 2)
3. Does the existing biological assessment program provide information to support an
agency action to assign the highest quality waters to different aquatic life use categories?
YES NO
If no, what changes to the type, amount, or quality of biological assessment information would
be useful? Would changes to data collection and analysis and/or internal communication
contribute to the use of biological assessments? Are there additional recommendations?
4. Does the existing biological assessment program currently provide information to support
agency decisions and actions (e.g., antidegradation policies, best management practices) to protect the
highest quality waters?
YES NO
If no, what changes to the type, amount, or quality of biological assessment information would
be useful? Would changes to data collection and analysis and/or internal communication
contribute to the use of biological assessments? Are there additional recommendations?
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WORKSHEET FOR TOPIC 2: PROTECTION OF CURRENT CONDITIONS
Example: A watershed with a mix of minimal to moderate impacts to aquatic systems from
anthropogenic stress. Streams, wetlands, lakes, and rivers support a range of biological
conditions based on biological indices (e.g., benthic macroinvertebrates, algal, and/or fish
assemblages). The presence of reproducing native species has been observed in waters where
there is minimal anthropogenic stress. Downstream waters such as bays and estuaries also
support a comparable range of biological conditions and levels of anthropogenic stress.
1. Does the existing biological assessment program provide information to detect declines
in biological condition?
YES NO
2. If yes to above, are the current indices sufficiently sensitive to detect incremental
declines within the assigned aquatic life use class?
YES NO
If no to either of the above questions, what changes to the type, amount, or quality of
biological assessment information would be useful? Would changes to data collection and
analysis and/or internal communication contribute to the use of biological assessments? Are
there additional recommendations?
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WORKSHEET FOR TOPIC 2: PROTECTION OF CURRENT CONDITIONS (page 2)
3. Does the biological assessment program provide information that the agency could use
to evaluate potential impacts on the aquatic community? (For example, a new and/or
modification to an existing industrial, transportation, or residential development is proposed
that might have an impact on aquatic life in the watershed.)
YES NO
If no, what changes to the type, amount, or quality of biological assessment information would
be useful? Would changes to data collection and analysis and/or internal communication
contribute to the use of biological assessments? Are there additional recommendations?
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WORKSHEET FOR TOPIC 2: PROTECTION OF CURRENT CONDITIONS (page 3)
4. If an evaluation for potential impacts indicates that the proposed activity would result in
a further decline in biological condition, would the biological assessment information used in
the evaluation support an agency action to minimize or prevent the predicted decline?
YES NO
If yes, what changes to the type, amount, or quality of biological assessment information would
be useful to provide better support?
If no, what changes to the type, amount, or quality of biological assessment information would
be useful? Would changes to data collection and analysis and/or internal communication
contribute to the use of biological assessments? Are there additional recommendations?
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WORKSHEET FOR TOPIC 3: PROTECTION OF IMPROVED CONDITIONS
Example: A watershed with mix of minimal to severe impacts from anthropogenic stress.
Streams, wetland, lakes, and rivers support a range of biological conditions from poor to
excellent based on biological indices (e.g., benthic macroinvertebrates, algal, and/or fish
assemblages). The presence of reproducing native species is documented only in higher quality
waters. Some of the severely impacted waters have been assigned a limited or modified aquatic
life use based on the findings of a use attainability analysis. Incremental improvements in
biological conditions in several water bodies have been observed. For a few of the severely
impacted waters, incremental improvements have been observed but conditions still do not
meet a higher use class. Downstream waters such as bays and estuaries also support a
comparable range of biological conditions and levels of anthropogenic stress.
1. Does the existing biological assessment program provide information to detect
incremental improvements in biological condition?
YES NO
2. If yes to above, are the current indices sufficiently sensitive to detect incremental
changes within the assigned aquatic life use class?
YES NO
If no to either of the two questions above, what changes to the type, amount, or quality of
biological assessment information would be useful? Would changes to data collection and
analysis and/or internal communication contribute to the use of biological assessments? Are
there additional recommendations?
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WORKSHEET FOR TOPIC 3: PROTECTION OF IMPROVED CONDITIONS (page 2)
3. Does the biological assessment program produce information to support an agency
decision to report and take action to protect improved aquatic life condition in a water body
where incremental improvements have been observed?
YES NO
If yes, please identify the specific management programs currently supported by biological
assessment data. Are there improvements to the type, quality, or delivery of the data that can
enhance use of the data?
If no, what changes to the type, amount, or quality of biological assessment information would
be useful? Would changes to data collection and analysis and/or internal communication
contribute to the use of biological assessments? Are there additional recommendations?
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WORKSHEET FOR TOPIC 4: SUPPORT USE CLASSIFICATION
Example: A watershed with a mix of minimal to severe impacts from anthropogenic stress.
Streams, wetlands, lakes, and rivers support range of biological conditions from poor to
excellent based on biological indices (e.g., benthic macroinvertebrates, algal, and/or fish
assemblages). The presence of reproducing native species in the higher quality waters is well
documented.
1. Does the biological assessment program produce information to support refining an
aquatic life use goal for water bodies?
YES NO
If no, what changes to the type, amount or quality of biological assessment information would
be useful? Would changes to data collection and analysis and/or internal communication
contribute to the use of biological assessments? Are there additional recommendations?
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SUMMARY WORKSHEET: SELF ASSESSMENT SESSION 1
Discussion Topics
1. Protect high quality waters
2. Protect current conditions
3. Protect improved conditions
4. Support for use classification
YES
NO
Summary observations and key recommendations:
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SELF-ASSESSMENT 2
Use of biological assessments to support water quality management programs
1. To answer these questions requires a thorough understanding of the information flow
and management decision-making process within and between programs in your
agency. In some cases this communication and decision-making may primarily occur at
the technical staff level, but in other cases it may occur between program managers
(e.g., between the permitting and the monitoring manager, or the water quality
standards coordinator and the monitoring manager) or even at the level of the water
Program Director or agency Commissioner.
The questions are most usefully answered during a cross-program group discussion
that includes representatives from all programs and levels of management.
2. For state agencies with aquatic life uses that are assessed using biological monitoring
data, it is helpful to estimate to what BCG level, or levels, your water quality agency's
aquatic life uses and numeric biological criteria provide protection;
To know this, the biological monitoring technical staff can determine (for example,
by a consensus of professional judgment) to what BCG level(s) your water quality
agency's biological criteria thresholds (e.g., numeric criteria, RBP, modeled index
(e.g. RIVPACS), or IBI ranges) provide protection. Alternatively, if your program does
not have numeric biological criteria, the staff can evaluate what BCG level your state
uses for listing biologically impaired waters. In other words, how does biologically-
based aquatic life use attainment measured by numeric biological criteria and/or
CWA section 303(d)-listing thresholds map to a BCG level?
3. The group answering this self-assessment should have some familiarity with your water
quality agency's application of biological criteria thresholds in regulatory decision-
making (i.e., be familiar with findings that have triggered an agency response based on
aquatic life use attainment/non-attainment as determined by biological assessment and
criteria).
4. Example scenarios characteristic of situations your agency encounters are
recommended to help focus the discussion and the identification of current strengths
and limitations of the biological assessment program.
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WORKSHEET FOR TOPIC 1: SUPPORT FOR WATER QUALITY STANDARDS
1. Does the biological assessment program provide data to support derivation of numeric
biological criteria?
YES NO
If yes, please list the water body types for which numeric biological criteria have been
developed:
Primary Headwater Streams YES NO
Streams YES NO
Rivers YES NO
Large Rivers YES NO
Lakes YES NO
Wetlands YES NO
Estuaries YES NO
Other (add below) YES NO
[water body type] YES NO
[water body type] YES NO
[water body type] YES NO
If yes to any of the above, are there improvements or refinements to the type, amount, quality,
or delivery of the data that would be useful? Please specify any recommendations for further
technical development.
If no to any of the above, what changes to the type, amount, or quality of biological assessment
information would be useful? Would changes to data collection and analysis and/or internal
communication contribute to the use of biological assessments? Are there additional
recommendations?
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WORKSHEET FOR TOPIC 1: SUPPORT FOR WATER QUALITY STANDARDS (page 2)
2. Does biological assessment information, whether from monitoring or from peer reviewed
literature, contribute to review of existing water quality criteria and/or to detection of the
need for new criteria or site-specific modifications?
YES NO
If no, what changes to the type, amount, or quality of biological assessment information would
be useful? Would changes to data collection and analysis and/or internal communication
contribute to the use of biological assessments? Are there additional recommendations?
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WORKSHEET FOR TOPIC 1: SUPPORT FOR WATER QUALITY STANDARDS (page 3)
3. Has your agency ever used biological assessments to assess effects or determine the need
for criteria for observed stressors for which there are no existing criteria?
Potential examples are listed below.
Habitat alteration YES NO
Water withdrawal/flow alterations YES NO
Suspended sediment YES NO
Nutrient effects YES NO
Other [list below if needed] YES NO
If no, what changes to the type, amount, or quality of biological assessment information would
be useful? Would changes to data collection and analysis and/or internal communication
contribute to the use of biological assessments? Are there additional recommendations?
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WORKSHEET FOR TOPIC 1: SUPPORT FOR WATER QUALITY STANDARDS (page 4)
4. During a triennial review, does the biological assessment program provide a list of waters
that are attaining biological conditions higher than their currently assigned aquatic life use?
YES NO
If no, what changes to the type, amount, or quality of biological assessment information would
be useful? Would changes to data collection and analysis and/or internal communication
contribute to the use of biological assessments? Are there additional recommendations?
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WORKSHEET FOR TOPIC 1: SUPPORT FOR WATER QUALITY STANDARDS (page 5)
5. Does the biological assessment program produce information to support designating a
water body to an antidegradation tier?
YES NO
If no, what changes to the type, amount, or quality of biological assessment information would
be useful? Would changes to data collection and analysis and/or internal communication
contribute to the use of biological assessments? Are there additional recommendations?
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WORKSHEET FOR TOPIC 2: SUPPORT FOR CWA SECTION 303(D) AND TMDL PROGRAMS
1. Does the biological assessment program provide data and information used to support
assessments for CWA section 303(d) purposes?
YES NO
If yes, what changes to the type, amount, or quality of biological assessment information
and/or the timing of data availability improve support to your program? (Please provide
specific recommendations.)
If no, what additional type, amount, or quality of biological assessment information would be
useful? Would changes to data collection and analysis and/or internal communication
contribute to the use of biological assessments? Are there additional recommendations?
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WORKSHEET FOR TOPIC 2: SUPPORT FOR CWA SECTION 303(D) AND TMDL PROGRAMS (page 2)
2. If biological assessment data has been used as the sole basis for putting one or more
waters on the 303(d) list (Category 5 of the Integrated Reporting Guidance [IRG]) for failure to
fully support the designated aquatic life use, was the non-support determination based on:
2a. Failure to meet a state numeric biological criteria? Or
2b. Conditions inconsistent with one or more narrative WQC?
YES NO
If yes for 2b, was the determination regarding failure to meet narrative water quality
criteria based on:
- Numeric biological thresholds issued as guidance values, rather than having been
incorporated into the state's WQS regulations
- Qualitative guidance on how to interpret biological assessment data
- Primarily, the best professional guidance of state agency staff
If yes for any of these aspects, what changes to the type, amount, or quality of biological
assessment information and/or the timing of data availability would improve use of biological
assessments as sole basis for 303(d) listing of water bodies?
If no, what changes to the type, amount, or quality of biological assessment information might
lead to use of biological assessments as the sole basis for 303(d) listing of water bodies?
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WORKSHEET FOR TOPIC 2: SUPPORT FOR CWA SECTION 303(D) AND TMDL PROGRAMS (page 3)
3. Has biological assessment data been used (in the absence of evidence of failure to meet
one or more chemical or physical water quality criteria) as the basis for making an affirmative
determination that one or more water bodies fully supports its designated aquatic life use, and
thereby belongs in Category 1 or 2 of the IRG? (Here "an affirmative determination of full
support" is intended to be distinguished from simply determining that available information
does not justify concluding that aquatic life use is NOT supported, which would call for putting
the water body in Category 3 of the IRG, as to aquatic life use.)
If yes, would changes to the type, amount, or quality of biological assessment information
improve support to your program? (Please provide specific recommendations.)
YES NO
If no, what changes to the type, amount, or quality of biological assessment information (in the
absence of evidence of failure to meet one or more chemical or physical water quality criteria)
might lead to use of biological assessments as the basis for declaring a water to be fully
supportive of its designated aquatic life use?
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WORKSHEET FOR TOPIC 2: SUPPORT FOR CWA SECTION 303(D) AND TMDL PROGRAMS (page 4)
4. Does the biological assessment program provide data and information used in support
of stressor identification analyses for waters identified as having impaired aquatic life use based
on biological assessments? If yes, were any individual (e.g., a particular pollutant or altered
flow) stressors identified? (Please list them.)
YES NO
If yes, were there any individual stressors for which biological assessment data was the sole
basis of identifying the stressors? (Please list these stressors.)
If there were no individual stressors identified using only biological assessment data:
How was biological assessment data used to supplement other kinds of data and
information in the course of identifying individual stressors? (If possible, answer on a
stressor-by-stressor basis)
What, if any, categories of stressors (e.g., heavy metals, PAHs, nutrients) were identified
using biological assessment data alone?
Would changes to the type, amount, or quality of biological assessment information and/or the
timing of data availability provide better support for stressor identification?
YES NO
If so, please provide specific recommendations on improvements to the biological assessment
program that would improve particular aspects of your stressor identification efforts.
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WORKSHEET FORTOPIC 2: SUPPORT FOR CWA SECTION 303(D) AND TMDL PROGRAMS (page 5)
5. Does the biological assessment program provide data and information to support
development of TMDLs?
YES NO
If yes, in which of the following aspects of TMDL development have biological assessment data
played a direct role?
Calculating of the overall water body-pollutant loading capacity:
Selecting a margin of safety:
Identifying sources of the pollutant of concern:
Allocating loads among existing and future sources:
Other aspects:
For any of these aspects, what changes to the type, amount, or quality of biological assessment
information and/or the timing of data availability would enable such information to play a
larger role? (If possible, answer on a TMDL function-by-function basis).
If no, what changes to the type, amount, or quality of biological assessment information and/or
the timing of data availability would enable such information to play a direct role in TMDL
development? (If possible, answer on a TMDL function-by-function basis.)
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WORKSHEET FOR TOPIC 3: SUPPORT FOR CWA SECTION 402 NPDES PROGRAM
1. Is biological assessment information used to support the CWA section 402 NPDES
program?
YES NO
If yes, how is the NPDES program supported by biological assessment information?
Impact assessment YES NO
Water quality-based effluent limits (WQBELs) YES NO
Mixing zone determination YES NO
WET limits and monitoring YES NO
Causal diagnosis YES NO
Other (please specify) YES NO
Would changes to the type, amount, or quality of biological assessment information and/or the
timing of data availability improve support to your program? (Please provide specific
recommendations.)
If no to any of the above questions, what additional type, amount, or quality of technical
information would be useful? Would changes to data collection and analysis and/or internal
communication contribute to the use of biological assessments? Are there additional
recommendations?
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WORKSHEET FOR TOPIC 3: SUPPORT FOR CWA SECTION 402 NPDES PROGRAM (page 2)
2. During NPDES permit reissuance, is information about biological condition downstream
of the point source reviewed for evidence of any need to evaluate and potentially change
permit limits to address observed problems? If yes, does the biological assessment program
provide data and information to support the NPDES program for this purpose?
YES NO
If yes, would changes to the type, amount or quality of biological assessment information
and/or the timing of data availability improve support to your program? (Please provide
specific recommendations.)
If no, what additional type, amount, or quality of technical information would be useful? Would
changes to data collection, data analysis, and/or internal communication (e.g., notification of
permit reissuance schedule) contribute to the use of biological assessments? Are there
additional recommendations?
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WORKSHEET FOR TOPIC 4: SUPPORT FOR CWA SECTION 319 PROGRAM
1. Does the biological assessment program provide data and information to support
implementation of the CWA section 319 program?
YES NO
If yes, would changes to the type, amount, or quality of biological assessment information
and/or the timing of data availability improve support to the program? (Please provide specific
recommendations.)
If not, what additional type, amount, or quality of technical information would be useful?
Would changes to data collection and analysis and/or internal communication contribute to the
use of biological assessments? Are there additional recommendations?
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WORKSHEET FOR TOPIC 5: SUPPORT FOR SECTION 401 CERTIFICATION
1. Does the biological assessment program provide data and information to support your
agency's section 401 certification program?
YES NO
If yes, would changes to the type, amount, or quality of biological assessment information
and/or the timing of data availability improve support to the program? (Please provide specific
recommendations.)
If not, what additional type, amount, or quality of technical information would be useful?
Would changes to data collection and analysis and/or internal communication contribute to the
use of biological assessments? Are there additional recommendations?
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WORKSHEET FOR TOPIC 6: SUPPORT FOR [insert program]
1. Does the biological assessment program provide data and information to support
implementation of ?
YES NO
If yes, would changes to the type, amount, or quality of biological assessment information
and/or the timing of data availability improve support to the program? (Please provide specific
recommendations.)
If not, what additional type, amount, or quality of technical information would be useful?
Would changes to data collection and analysis and/or internal communication contribute to the
use of biological assessments? Are there additional recommendations?
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SUMMARY WORKSHEET: SELF ASSESSMENT 2
Discussion Topics
1. Water Quality Standards
2. CWA section 303(d) and TMDL
Programs
3. CWA section 402 NPDES
Programs
4. CWA section 319 NPS Programs
5. CWA section 401 certification
6.
7.
8.
YES
NO
Summary observations and key recommendations:
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APPENDIX D: TECHNICAL MEMORANDUM TEMPLATE
TECHNICAL MEMORANDUM
Technical Elements Evaluation of the [State/Tribal] Biological Assessment Program
[State/Tribal Agency]
[Location]
[Dates of Third Party Assessment]
Purpose:
To evaluate the technical program and to make recommendations for enhancements relative to
design, methodology, and execution for credible data as a basis of making informed decisions
regarding the ecological condition of [state/tribal agency's] surface waters.
Attendance:
Agency Participant Contact, Organization, (email) Phone Number (XXX) (XXX-XXXX)
[List all state/tribal agency and U.S. Environmental Protection Agency (EPA) attendees]
Basis for Evaluation
Since 1990, EPA has supported the development of water quality agency biological assessment
programs via the production of methods documents, case studies, regional workshops, and
evaluations of individual water quality agency programs. EPA recommends that states and
tribes use biological assessments to more precisely define their designated aquatic life uses and
adopt numeric biological criteria necessary to protect those uses (USEPA 1990, 1991).
Overview and Summary of [State/Tribal Agency] Program and Significant Issues
The [date of evaluation] evaluation of the [state/tribal agency] biological assessment program
addressed a range of topics, as summarized below. A biological program review was also
completed using a standardized checklist and scoring methodology. The results are discussed as
part of this memorandum.
Please provide a detailed summary of the agency's program for the flowing topics:
A. Monitoring and Assessment Program
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B. Water Quality Standards (WQS): Designated Uses
C. Delineation of Impaired Waters
Biological assessment program evaluation
The following is a description of the current status of the program and the results of the
technical elements evaluation.
Biological assessment program description
Please provide a detailed summary of the state's biological assessment program.
Critical elements evaluation
A biological program review was conducted by proceeding through the technical elements
checklist (Appendix E) in accordance with the methodology described in The Biological Program
Review: Assessing Level of Technical Rigor to Support Water Quality Management (EPA 820-R-
13-001. The document includes a description of 13 technical elements of a biological
assessment program, the checklist for evaluating the level of technical development for each
element, and a method for characterizing the overall level of program rigor. The [water quality
agency] critical elements evaluation yielded a raw score of out of a maximum possible score
of 52. This is a Level program (range - ). The critical technical elements of biological
assessment programs are described and divided into four general levels of technical
development with Level 4 the highest level of rigor. A Level 4 program is able to provide the
most comprehensive support for a water quality management program. As a technical program
is improved, biological assessment information can be used with increasing confidence to
support multiple water quality program needs for information. These needs include more
precisely defined aquatic life uses and approaches for deriving biological criteria, supporting
causal analysis, and developing stressor-response relationships.
Highlights of each element are indicated in Table D-l (hypothetical example shown). The
improvements that are needed to elevate the score for each element are described by element
in the same order that they appear in the attached checklist as follows:
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Table D-l. Example review results: The following recommendations were made to a state water
quality agency as a result of their critical elements evaluation
Element
Comment
Element 1: Index Period
Score assigned = 2.0
The score of2.0 reflects a varied adherence to a seasonal index
period. Logistical bottlenecks seem to be the principal reason
for deviations that can extend into the following spring of each
year. Elevating the score for this element will require a strict
adherence to the August 15-November 15 index period.
Element 2: Spatial Sampling Design
Score assigned = 2.0
The score of 2.0 conservatively reflects the synoptic design and
spatial density of sampling sites that is employed. Elevating the
score to the maximum of 4.0 will require a greater spatial
density within watershed assessment units particularly getting
beyond the "pour point" as the only sampling site on a river or
stream.
Element 3: Natural Variability
Score assigned = 2.0
The CE score of 2.0 should be elevated to 4.0 with the
developments that are already underway including the addition
of new regional reference sites and the fuller inclusion of the
other bioregions.
Element 4: Reference Site Selection
Score assigned = 3.0
As criteria are further refined (site-scoring process) for
reference sites, the CE score of 3.0 should improve to 4.0
because it is being employed in the selection of new regional
reference sites.
Element 5: Reference Conditions
Score assigned = 3.0
The CE score of 3.0 should improve to 4.0 with the additional
regional reference sites that are being established as part of
the ongoing improvements described for elements 3 and 4.
Element 6: Taxa and Taxonomic Resolution
Score assigned = 3.0
The CE score of 3.0 reflects the full development of the
macroinvertebrate assemblage and the in progress
development of a second and third assemblage. Reaching the
CE score of 4.0 is contingent on the full development and use
of a second assemblage.
Element 7: Sample Collection
Score assigned = 3.0
The CE score of 3.0 reflects the full development of the
macroinvertebrate assemblage (i.e., for the mountain region
only) and the in-progress development of a second and third
assemblage. Reaching the CE score of 4.0 is contingent on the
full development and use of a second assemblage and for all
applicable bioregions.
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Element
Comment
Element 8: Sample Processing
Score assigned = 3.0
The CE score of 3.0 reflects the full development of the
macroinvertebrate assemblage for the mountain bioregion and
the in progress development of the other bioregions and a
second and third assemblage. Reaching the CE score of 4.0 is
contingent on the full development and use of a second
assemblage.
Element9: Data Management
Score assigned = 3.0
The CE score of 3.0 can be improved to 4.0 once the data
management system includes all data (i.e., habitat and fish)
and is readily accessible.
Element 10: Ecological Attributes
Score assigned = 2.0
The CE score of 2.0 should increase with the development of
the macroinvertebrate multimetric index (MMI) for all
bioregions. A descriptive analysis of the biological condition
gradient (BCG) for each representative bioregion and
application of these concepts to the full development of the
biological indicators and assemblages will improve the score to
4.0.
Element 11: Discriminatory Capacity
Score assigned = 2.0
The CE score of 2.0 will be increased to at least 3.0 with the full
development of the macroinvertebrate MMI and the derivation
of appropriately detailed numeric biological criteria. Achieving
a score of 4.0 will require that this be accomplished for a
second biological assemblage.
Element 12: Stressor Association
Score assigned = 2.0
The comparatively low CE score of 2.0 is a common
characteristic of biological assessment programs that are in
development and/or which have singularly been focused on
status assessments with no or limited coordination with other
environmental assessments. Improving the score for this
element will occur as a result of addressing preceding elements
2, 3, 6,10, and 11 and gaining a familiarity with how diagnostic
capacity is developed. This will require some dedication to
exploratory analyses in which the response of the biological
assemblages is evaluated along the stressor axis of the BCG.
Element 13: Professional Review
Score assigned = 2.0
The CE score of 2.0 can be elevated to 4.0 by instituting a more
formal peer review process and by publishing some of the
ongoing developments in peer reviewed journals.
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Critical Elements Summary
Please provide a detailed summary of the agency's critical elements performance and include a
discussion of ongoing program improvements that will increase the rigor of the agency's
biological assessment program.
Recommendations
Summary of recommendations to the agency on how to improve the rigor of its biological
assessment program and recommendations for program enhancements to support more
comprehensive and efficient use of biological assessments in an agency's water quality
program.
Citations
USEPA (U.S. Environmental Protection Agency). 1990. Biological Criteria: National Program for
Surface Waters. EPA 440-5-90-004. U.S. Environmental Protection Agency, Office of
Water, Washington, DC. . Accessed October
2012.
USEPA (U.S. Environmental Protection Agency). 1991. Policy on the Use of Biological
Assessments and Criteria in the Water Quality Program. U.S. Environmental Protection
Agency, Washington, DC.
. Accessed February 2013.
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APPENDIX E. TECHNICAL ELEMENTS CHECKLIST
The following is a checklist for evaluating the degree of development for each technical
element of a biological assessment program and associated comments on the elements for the
[water quality agency] biological assessment program. The point scale for each element ranges
from lowest to highest resolution.
|H||jjj|a (Lowest) 1.0 2.0 3.0 4.0 (Highest)
Index Period
Temporal
variability is not
taken into
account.
Sampling period
established based
on practices of
other agencies
and/or literature.
Sampling outside
the index is not
adjusted for
temporal
influence.
Index period
established based
on o priori
assumptions
regarding temporal
variability of
biological
community. Effects
of the use of index
period are
documented. Data
collected outside
the index period
data might be
adjusted to correct
for temporal
influences.
Temporal
variability is fully
characterized and
taken into account
for all data. Agency
information needs
and index periods
are coordinated so
that adherence to
an index period is
strict.
Comments
Points
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Study design
consisting of
isolated, single,
fixed-point sites.
Low density fixed
station design.
Multiple sites are used
for assessment of a
water body or
watershed condition.
Spatial coverage
suitable for general
condition assessments.
Non-random designs
at coarse scale used
(e.g., 4-8 digit
hydrologic unit code
[HUC]). Inference of
site data to larger unit
of assessment based
on "rules of thumb"
and might be
supplemented by
upstream/downstream
assessments.
Low density
random or
stratified random
sampling design
which allows for a
statistically valid
inference of
biological
condition to a
spatial unit larger
than a site. The
primary goal is to
assess aggregate
condition and
trends on a
statewide or
regional basis.
High density (e.g.,
intensive)
monitoring at
comprehensive
spatial sampling
design suitable for
watershed
assessments (e.g.,
10-12 digit HUC)
and in support of
multiple water
quality
management
program needs
for information
(e.g., condition
assessments, use
refinement, use
attainability
analyses [UAAs],
permits). As
needed, the
spatial sampling
combines
monitoring
designs to
optimize cost and
efficiency in data
collection and
analysis (e.g.,
combination of
upstream-
downstream,
intensive,
probabilistic,
and/or pollution
gradient designs).
Typically includes
a rotating
sequence of
watershed units
organized to
provide data for
management
program support.
Comments
Points
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No or minimal
partitioning of
natural
variability in
aquatic
ecosystems.
Does not
incorporate
differences in
watershed
characteristics
such as size,
gradient,
temperature,
elevation, etc.
Classification
scheme is based on
assumed, first-order
classes. These
include strata such
as fishery-based cold
or warmwater
classes. There is no
formal consideration
of regional strata
such as bioregions
or aggregated
ecoregions. Intra-
regional strata such
as watershed size,
gradient, elevation,
temperature are not
addressed. Usually
applied uniformly on
a statewide basis.
A fully partitioned
and stratified
classification
scheme or
modeling
approach is
employed. Classes
and/or continuous
models are
defined to take
critical details of
spatial variability
into account.
Inter-regional
landscape features
and phenomena
are appropriately
sequenced with
intra-regional
strata.
Subcategories of
lotic ecotypes are
defined (e.g.,
includes the full
strata of lotic
water body types).
Characterization of
spatial variability is
confined within
jurisdictional
boundaries.
Scheme to fully
account for
natural variation is
periodically
refined and
updated as new
data and methods
become available.
Classes,
continuous
models, or both,
are examined to
identify the most
appropriate
scheme for
monitoring and
assessment,
regulatory
support, and cost-
effectiveness.
Developed at
scales that
transcend
jurisdictional
boundaries when
necessary to
strengthen inter-
regional
classification
outcomes;
recognizes the full
zoogeographical
aspects of
biological
assemblages.
Comments
Points
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Reference Si
Informal best
professional
judgment (BPJ)
used in selection
of control sites.
No screens are
used. Limited, if
any,
documentation
and supporting
rationale.
Based on "best
biology" (i.e., BPJ on
what the best
biology is in the best
water body).
Minimal non-
biological data used.
Minimal
documentation.
Selection based on
narrative
descriptions of
non-biological
characteristics.
Combines BPJ with
narrative
description of land
use and site
characteristics.
Might use
chemical and
physical data
thresholds as
primary filters.
Based on
quantitative
descriptions of
non-biological
characteristics
with primary
reliance on abiotic
data on landscape
conditions and
land use. Chemical
and physical data
might be used as
secondary filters
or in a hybrid
approach for
severely altered
landscapes.
Independent data
set used for
validation.
Comments
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No reference
condition has
been developed.
Biological data
are assessed
using BPJ or
based on the
presence of
targeted or
iconic taxa.
Reference
condition based on
biology of an
estimated 'best'
site or water body.
Single reference
sites are used to
assess biological
data collected
throughout a
watershed. A site-
specific control or
paired watershed
approach might be
used.
Reference
condition is based
on a regional
aggregate of
reference site
information. Data
representing most
of the major
natural
environmental
gradients but
limited in number
and/or spatial
density. Overall
number and
coverage of
reference sites
insufficient to
support statistical
evaluation of the
biological condition
at test sites.
Reference
condition is based
on data from
many reference
sites that span all
major natural
environmental
gradients in the
study area.
Reference
condition can be
estimated for
individual sites by
modeling biota-
environmental
relationships. The
number of
reference sites is
sufficient to
support statistical
evaluation of
biological
condition at test
sites. Reference
sites are
resampled
periodically. In
highly altered
regions or water
body types,
alternative
methods are used
to develop
reference
condition.
Comments
Points
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c
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One taxonomic
assemblage (e.g.,
benthic
macroinvertebrates,
fish, algae, aquatic
macrophytes). Very
coarse taxonomic
resolution (e.g.,
order/family).
Expertise: amateur
naturalist or stream
watcher. Validation:
none. QA/QC: none.
One taxonomic
assemblage. Low
taxonomic resolution
(e.g., family).
Expertise: novice or
apprentice biologist.
Validation: family
level certification for
macroinvertebrates.
No certification
available for fish or
algae. QA/QC:
mostly for taxonomic
confirmation of
voucher collections.
Some sorting QA/QC
implemented.
One taxonomic
assemblage. Fine
taxonomic
resolution:
genus/species for
benthic
macroinvertebrates
and algae, species
for fish. Expertise:
trained taxonomist.
Validation: genus-
level certification or
equivalent for
benthic
macroinvertebrates.
Expert fish
taxonomist or
equivalent. Formal
courses or training
in algal taxonomy.
QA/QC: addresses
measuring bias,
precision, and
accuracy in all
phases of sample
processing through
identification (e.g.,
outside validation
of identification);
voucher collection
maintained.
Same as Level 3
except that two
or more
taxonomic
assemblages
are assessed.
Rationale for
selection of
taxonomic
groups should
be well
documented.
Comments
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01
3
01
Q.
£
ra
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Approach is
cursory and
relies on
operator skill
and BPJ.
Training limited
to that which is
conducted
annually for
non-biologists
who compose
the majority of
the sampling
crew. Methods
are not
systematically
documented as
standard
operating
procedures
(SOPs).
Textbook
methods are used
without
considering the
applicability of the
methods to the
study area. SOPs
to specify
methods but
methods are
neither well
documented nor
evaluated for
producing
comparable data
across agencies. A
cursory QA/QC
document might
be in place.
Training consists
of short courses
(1-2 days) and is
provided for new
staff and
periodically for all
staff.
Methods are
evaluated for
applicability to
study area and
refined (if
needed).
Detailed and well
documented
SOPs are
I I r\r\ f\ + r\r\
updated
periodically and
supported by in-
house testing
and
development. A
formal QA/QC
program is in
place with field
replication
requirements.
Rigorous training
required for all
professional
staff.
Same as Level 3, but
methods cover multiple
assemblages. A field
audit of sampling crews
is performed annually to
ensure that protocols
and proper sample
handling/documentation
are followed.
Comments
Points
||jjjjj|j|a (Lowest) 1.0 2.0 3.0 4.0 (Highest)
M
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a
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Q.
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Organisms are
sorted,
identified, and
counted in the
field using
dichotomous
keys.
Organisms are
sorted, identified,
and counted
primarily in the field
by trained staff.
Adequate QA/QC is
not possible. For
fish, cursory
examination of
presence and
absence only.
Agency SOPs not
developed or
published.
All samples
(except for fish)
are processed in
the laboratory. A
formal QA/QC
program is in
place. Rigorous
training is
provided. Voucher
organisms are
retained for ID
verification. SOPs
are published and
available to
others.
Same as Level 3,
but applied to
multiple
assemblages.
Subsampling level
is tested. Presence
offish
deformities,
erosions, lesions,
tumors (DELT) and
other anomalies
are quantified and
documented.
Comments
Points
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Management
ra
Q
Sampling event
data organized in
a series of
spreadsheets
(e.g., by year, by
data-type).
QA/QC is cursory
and mostly for
transcription
errors. Might be
paper files only.
Databases for
physical-chemical,
and biological data,
and geographic
information exist
(Access, dBase,
Geographic
Information System
[CIS], etc.) but are
not linked or
integrated. Data-
handling methods
manuals are
available. QA/QC for
data entry, value
ranges, and site
locations. A
documented data
dictionary defines
data fields in terms
of field methods and
data collection.
Relational
databases that
integrate all
biological,
physical, and
chemical data
(Oracle, SQL
Server, Access,
etc.). Validation
checks that guard
against
inadvertently
storing incorrect
or incomplete
sampling data.
Fully documented
and implemented
QA/QC process.
Structure provides
for data export
and analysis via
query includes
dedicated
database
management. Fully
documented data
dictionary. Access
to all databases is
available for
routine analysis in
support of
condition
assessment.
Same as Level 3
adding automated
data review and
validation tools.
Numerous built-in
data management
and analysis tools
to support routine
and exploratory
analyses. Ability to
track history of
changes made to
the data. Ability to
control who has
privilege to
change, update, or
delete data. Data
import and export
tools. Integrated
connection to GIS
showing
monitored sites in
relation to other
relevant spatial
data layers. Fully
documented
metadata
according to
accepted database
standards. Reports
on commonly
used endpoints
are easily
retrieved (e.g.,
menu driven).
Comments
Points
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V)
01
M
3
.Q
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5
Ecological
Biological
program relies
solely on the
evaluation of the
presence or
absence of
targeted or key
species. No
rationale is
provided for
selection of
indicators.
Assessment
endpoints and
ecological
attributes are not
defined.
Biological program
based on "off the
shelf indicators for
one biological
assemblage.
Rationale for
selection of
indicators is partially
documented.
Generic assessment
endpoints and
ecological attributes
are defined but not
specifically
evaluated for state
or regional
conditions.
Biological program
based on well-
developed
ecological
attributes for one
biological
assemblage.
Rationale for
attribute selection
is thorough and
well-documented.
Explicit linkage is
provided between
management goal,
assessment
endpoints, and
ecological
attributes.
Same as Level 3,
but biological
program based on
well-developed
ecological
attributes for two
or more biological
assemblages (e.g.,
faunal, flora) for
more complete
assessment of the
members of an
aquatic
community.
Comments
Points
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Coarse method
(low signal) and
detects only high
and low values.
Supports
distinguishing
only extreme
change in
biological
condition at the
upper and lower
ends of a
generalized
stress gradient.
A biological index
for one assemblage
is established but is
not calibrated for
water body classes,
regional or
statewide
applications. BPJ
based on single
dimension
attributes. The index
can distinguish two
general levels of
change in biological
condition along a
generalized stress
gradient.
A biological index
for one
assemblage has
been developed
and calibrated for
statewide or
regional
application and for
all classes and
strata of a given
water body type.
The index can
distinguish 3 to 4
increments of
biological change
along a continuous
stress gradient.
Supports narrative
evaluations (e.g.,
good, fair, poor)
based on
multimetric or
multivariate
analyses that are
relevant to the
selected ecological
attributes
(Technical
Element 10).
Same as Level 3
but biological
indices for two or
more assemblages
have been
developed and
calibrated.
Additionally, the
indices can
distinguish finer
increments of
biological change
along a
continuous stress
gradient. The
number of
increments that
potentially can be
distinguished is
dependent on
water body type
and natural
climatic and
geographic
factors.
Comments
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_o
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K
No ability to
develop
relationships
between
biological
responses and
anthropogenic
stress.
Site-specific paired
biological and
stressor samples for
studies of an
individual water body
or a segment of a
water body (e.g., a
stream reach). Stress-
response
relationships are
developed based on
assemblage attributes
at coarse level
taxonomy (e.g.,
family for benthic
macroinvertebrates).
Information might be
used on a case-by-
case basis to inform a
first order causal
analysis.
Low spatial
resolution for
paired biological
and stressor
samples in time and
space across the
state at basin or
sub-basin scale
(e.g., HUC4-8).
Stress-response
relationships
developed for one
assemblage using
regression analysis.
Taxonomy at level
sufficient to detect
patterns of
response to stress
(e.g., species or
genus for benthic
macroinvertebrates
or periphyton,
species for fish).
Relational database
supports basic
queries.
Information is
frequently used to
inform causal
analysis.
Reevaluation of
stress-response
relationships on an
as-needed basis.
High spatial
resolution for
paired biological
(including DELT
anomalies and
other indicators of
organism health)
and stressor
samples in time and
space across the
state at watershed
or subwatershed
scales (e.g., HUC
10-12). Other data
(e.g., watershed
characteristics, land
use data and
information, flow
regime, habitat,
climatic data) are
linked to field data
for source
identification.
Stress -response
relationships are
fully developed for
two or more
assemblages,
stressors, and their
sources using a
suite of analytical
approaches (e.g.,
multiple regression,
multivariate
techniques).
Relational database
supports complex
queries.
Information is
routinely used to
inform causal
analysis and criteria
development.
Ongoing evaluation
of stress- response
relationships and
monitoring for new
stressors is
supported.
Comments
Points
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Review
ra
c
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8
Q.
Review is limited
to editorial
aspects. No
technical review.
Internal technical
review only.
Outside review of
documentation
and reports are
conducted on an
ad hoc basis.
Formal process for
technical review
to include multiple
reference and
documented
system for
reconciliation of
comments and
issues. Process
results in methods
and reporting
improvements.
Can include
production of
peer-reviewed
journal
publications by
the agency.
Comments
Points
144
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