United States
Environmental Protection
Agency
n of Estuaries
I
A Statistical Summary
ARCH AND
LOP
-------
-------
EPA 620/R-04/200
February 2005
Condition of Estuaries of the Western United
States for 1999: A Statistical Summary
Office of Research and Development
U.S. Environmental Protection Agency
Washington, DC 20460
-------
List of Authors
Walter G. Nelson1, Henry Lee II1, Janet 0. Lamberson1, Virginia Engle2, Linda Harwell2,
Lisa M. Smith2
List of Author Affiliations
1 Western Ecology Division, National Health and Environmental Effects Research
Laboratory, U.S. Environmental Protection Agency, Newport OR 97365
2 Gulf Ecology Division, National Health and Environmental Effects Research
Laboratory, U.S. Environmental Protection Agency, Gulf Breeze FL 32561
-------
Preface
This document is the statistical summary for the western states, coastal component of
the nationwide Environmental Monitoring and Assessment Program (EMAP). The focus
of the study during 1999 was the small estuaries of Washington, Oregon, and California
(excluding Puget Sound, the main channel of the Columbia River, and San Francisco
Bay). EMAP-West is a partnership of the States of California, Oregon and Washington,
the National Oceanic and Atmospheric Administration (NOAA), and the U.S.
Environmental Protection Agency (EPA). The program is administered through the EPA
and implemented through partnerships with a combination of federal and state
agencies, universities and the private sector.
The appropriate citation for this report is:
Nelson, Walter G., Lee II, Henry, Lamberson, Janet 0., Engle, Virginia, Harwell,
Linda, Smith, Lisa M. 2004. Condition of Estuaries of Western United States for
1999: A Statistical Summary. Office of Research and Development, National
Health and Environmental Effects Research Laboratory, EPA/620/R-04/200.
Disclaimer
The information in this document has been funded wholly or in part by the U.S.
Environmental Protection Agency under Cooperative Agreements with the states of
Washington (CR 827869 ), Oregon (CR 87840 ), and California (CR 827870 ) and an
Inter Agency Agreement with the National Marine Fisheries Service (DW 13938780). It
has been subjected to review by the National Health and Environmental Effects
Research Laboratory and approved for publication. Approval does not signify that he
contents reflect the views of the agency, nor does mention of trade names or
commercial products constitute endorsement or recommendation for use.
-------
Acknowledgments
Western Coastal EMAP involves the cooperation of a significant number of federal,
state, and local agencies. The project has been principally funded by the U.S.
Environmental Protection Agency Office of Research and Development. The following
organizations provided a wide range of field sampling, analytical and interpretive
support in their respective states through individual cooperative agreements with EPA:
Washington Department of Ecology, Oregon Department of Environmental Quality,
Southern California Coastal Water Research Project (SCCWRP). The Northwest
Fisheries Science Center, National Marine Fisheries Service, National Oceanic and
Atmospheric Administration provided field support and analysis offish pathologies
through a cooperative agreement with EPA. Other research organizations provided
additional scientific support through subcontracts with these lead organizations. Moss
Landing Marine Laboratory provided the field crews for collection of samples in
California under contract to SCCWRP.
The U.S. Geological Survey, Columbia Environmental Research Center, through the
Biomonitoring Environmental Status and Trends (BEST) Program, provided analyses for
H4IIE bioassay-derived 2,3,7,8-tetrachlorodibenzo - p -dioxin equivalents (TCDD-EQ)
for exposure of fish to planar halogenated hydrocarbons. Through their Marine
Ecotoxicology Research Station, BEST also provided two bioassays on sediment
porewater toxicity, the sea urchin Arbacia punctulata fertilization toxicity and embryo
development toxicity tests.
Project wide information management support was provided by SCCWRP as part of
their cooperative agreement.
Many individuals within EPA made important contributions to Western Coastal EMAP.
Critical guidance and vision in establishing this program was provided by Kevin
Summers of Gulf Ecology Division. Tony Olsen of Western Ecology Division (WED) has
made numerous comments which have helped to improve the quality of this document.
Lorraine Edmond of the Region 10 Office of EPA and Terrence Fleming of the Region 9
Office of EPA have ably served as the regional liaisons with the state participants in
their regions. Robert Ozretich of WED performed a detailed review of the database
contents used for this analysis, and we additionally thank him for his extensive quality
assurance review of this document.
We thank Jeff Hyland of NOAA and Joan Cabreza of the Region 10 Office of EPA for
their technical reviews of this report.
The success of the Western Coastal pilot has depended on the contributions and
dedication of many individuals. Special recognition for their efforts is due the following
participants:
IV
-------
Washington Department of Ecology
Casey Cliche
Margaret Dutch
Ken Dzinbal
Christina Ricci
Kathy Welch
Oregon Department of Environmental Quality
Mark Bautista
Greg Coffeen
Curtis Cude
Paula D'Alfonso
RaeAnn Haynes
Dan Hickman
Bob McCoy
Greg McMurray
Greg Pettit
Chris Redmond
Crystal Sigmon
Daniel Sigmon
Scott Sloane
Southern California Coastal Water Research Project (SCCWRP)
Larry Cooper
Steve Weisberg
Moss Landing Marine Laboratory
Russell Fairey
Cassandra Roberts
San Francisco Estuary Institute
Bruce Thompson
University of California Davis
Brian Anderson
National Oceanic and Atmospheric Administration
National Marine Fisheries Service, Northwest Fisheries Science Center
Bernie Anulacion
Tracy Collier
Dan Lomax
Mark Myers
Paul Olson
-------
U.S. Geological Survey
Biomonitoring of Environmental Status and Trends Program (BEST)
Christine Bunck
Columbia Environmental Research Center
Don Tillet
Marine Ecotoxicology Research Station
Scott Carr
Gulf Breeze Project Office
Tom Heitmuller
Steve Robb
Pete Bourgeois
U.S. Environmental Protection Agency
Office of Research and Development
Tony Olsen
Steve Hale
John Macauley
Region 9
Terrence Fleming
Janet Hashimoto
Region 10
Lorraine Edmond
Gretchen Hayslip
Indus Corporation
Patrick Clinton
VI
-------
Table of Contents
Preface iii
Disclaimer iii
Acknowledgments iv
List of Figures x
List of Tables xiv
Executive Summary xvi
1.0 Introduction 1
1.1 Program Background 1
1.2 The Western United States Context for
a Coastal Condition Assessment 2
1.3 Objectives 3
2.0 Methods 5
2.1 Sampling Design and Statistical Analysis Methods 5
2.1.1 Background 5
2.1.2 Sampling Design 6
2.1.2.1 1999 West Coast Design 6
2.1.2.2 2000 West Coast Design 8
2.2 Data Analysis 21
2.3 Indicators 24
2.3.1 Water Measurements 27
2.3.1.1 Hydrographic Profile 27
2.3.1.2 Water Quality Indicators 28
vii
-------
2.3.2 Sediment Toxicity Testing 29
2.3.2.1 Sediment Collection 29
2.3.2.2 Laboratory Test Methods 30
2.3.2.2.1 Amphipod Toxicity Tests 30
2.3.2.2.2 Sea Urchin Toxicity Tests 31
2.3.3 Biotic Condition Indicators 32
2.3.3.1 Benthic Community Structure 32
2.3.3.2 Fish Trawls 33
2.3.3.3 Fish Community Structure 34
2.3.3.4 Fish Contaminant Sampling 34
2.3.3.5 Fish Contaminant Chemistry Analyses 35
2.3.3.6 Fish Gross Pathology 36
2.3.4 Sediment Chemistry 36
2.4 General QA/QC Process 41
2.4.1 QA of Chemical Analyses 42
2.4.2 QA of Taxonomy 50
2.5 Data Management 52
2.6 Unsamplable Area 52
3.0 Indicator Results 55
3.1 Habitat Indicators 55
3.1.1 Salinity 55
3.1.2 Water Temperature 55
3.1.3 pH 55
viii
-------
3.1.4 Sediment Characteristics 56
3.1.5 Water Quality Parameters 56
3.1.6 Water Column Stratification 57
3.2 Exposure Indicators 73
3.2.1 Dissolved Oxygen 73
3.2.2 Sediment Contaminants 73
3.2.2.1 Sediment Metals 73
3.2.2.2 Sediment Organics 91
3.2.3 Sediment Toxicity 99
3.2.3.1 Ampelisca abdita 99
3.2.3.2 Arbacia punctulata 99
3.2.4 Tissue Contaminants 108
3.3 Biotic Condition Indicators 115
3.3.1 Infaunal Species Richness and Diversity 115
3.3.2 Infaunal Abundance and Taxonomic Composition 116
3.3.3 Demersal Species Richness and Abundance 124
4.0 References 129
IX
-------
List of Figures
Figure 2-1. Location of Washington EMAP survey sites 10
Figure 2-2. Location of EMAP survey sites along the northern portion
of the Oregon coast, including survey sites for the intensification study of
Tillamook Bay 11
Figure 2-3. Location of EMAP survey sites along the southern portion
of the Oregon coast 12
Figure 2-4. Location of EMAP survey sites for the intensification study
of Tillamook Bay, Oregon 13
Figure 2-5. Location of California EMAP survey sites in Northern California
from the Oregon Border to the Garcia River 14
Figure 2-6. Location of California EMAP survey sites in Northern and
Central California from the Russian River to the Santa Ynez River 15
Figure 2-7. Location of California EMAP survey sites in Central and
Southern California from Santa Barbara to the Mexican border 16
Figure 3.1-1. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. salinity of bottom waters 58
Figure 3.1-2. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. temperature of bottom waters 59
Figure 3.1-3. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. pH in bottom waters 60
Figure 3.1-4. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. percent silt-clay of sediments 61
Figure 3.1-5. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. percent total organic carbon of sediments 62
Figure 3.1-6. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. water column mean concentration of chlorophyll a. . . 63
Figure 3.1-7. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. water column mean nitrate + nitrite concentration. ... 64
-------
Figure 3.1-8. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. water column mean ammonium concentration 65
Figure 3.1-9. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. water column mean total nitrogen
(nitrate + nitrite + ammonium) concentration 66
Figure 3.1-10. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. water column mean orthophosphate concentration. . . 67
Figure 3.1-11. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. water column mean ratio of total nitrogen
(nitrate + nitrite + ammonium) concentration to total orthophosphate
concentration 68
Figure 3.1-12. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. water column total suspended solids concentration. . 69
Figure 3.1-13. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. percent light transmission estimated
at a reference depth of 1 m in the water column 70
Figure 3.1-14. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. water column stratification index 71
Figure 3.1-15. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. Aot stratification index 72
Figure 3.2-1. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. dissolved oxygen of bottom waters 74
Figure 3.2-2. Percent area (and 95% C.I.) of small estuaries of the
West Coast states vs. dissolved oxygen of surface waters 75
Figure 3.2-3. Percent area (and 95% C.I.) of West Coast small estuaries
vs. sediment concentration of arsenic 80
Figure 3.2-4. Percent area (and 95% C.I.) of West Coast small estuaries
vs. sediment concentration of cadmium 81
Figure 3.2-5. Percent area (and 95% C.I.) of West Coast small estuaries
vs. sediment concentration of chromium 82
XI
-------
Figure 3.2-6. Percent area (and 95% C.I.) of West Coast small estuaries
vs. sediment concentration of copper 83
Figure 3.2-7. Percent area (and 95% C.I.) of West Coast small estuaries
vs. sediment concentration of lead 84
Figure 3.2-8. Percent area (and 95% C.I.) of West Coast small estuaries
vs. sediment concentration of mercury 85
Figure 3.2-9. Percent area (and 95% C.I.) of West Coast small estuaries
vs. sediment concentration of nickel 86
Figure 3.2-10. Percent area (and 95% C.I.) of West Coast small estuaries
vs. sediment concentration of selenium 87
Figure 3.2-11. Percent area (and 95% C.I.) of West Coast small estuaries
vs. sediment concentration of silver 88
Figure 3.2-12. Percent area (and 95% C.I.) of West Coast small estuaries
vs. sediment concentration of tin 89
Figure 3.2-13. Percent area (and 95% C.I.) of West Coast small estuaries
vs. sediment concentration of zinc 90
Figure 3.2-14. Percent area (and 95% C.I.) of West Coast small estuaries
vs. sediment concentration of total PAHs 94
Figure 3.2-15. Percent area (and 95% C.I.) of West Coast small estuaries vs. sediment
concentration of high molecular weight PAHs 95
Figure 3.2-16. Percent area (and 95% C.I.) of West Coast small estuaries vs. sediment
concentration of low molecular weight PAHs 96
Figure 3.2-17. Percent area (and 95% C.I.) of West Coast small estuaries
vs. sediment concentration of total PCBs 97
Figure 3.2-18. Percent area (and 95% C.I.) of West Coast small estuaries
vs. sediment concentration of total DDT 98
Figure 3.2-19. Percent area (and 95% C.I.) of West Coast small estuaries
vs. percent control corrected survivorship of Ampelisca abdita 101
XII
-------
Figure 3.2-20. Percent area (and 95% C.I.) of West Coast small estuaries vs. percent
fertilization of Arbacia punctulata eggs for the 100% water quality adjusted
porewater concentration 102
Figure 3.2-21. Percent area (and 95% C.I.) of West Coast small estuaries vs. percent
fertilization of Arbacia punctulata eggs for the 50% water quality adjusted
porewater concentration 103
Figure 3.2-22. Percent area (and 95% C.I.) of West Coast small estuaries vs. percent
fertilization of Arbacia punctulata eggs for the 25% water quality adjusted
porewater concentration 104
Figure 3.2-23. Percent area (and 95% C.I.) of West Coast small estuaries vs. percent
successful embryonic development of Arbacia punctulata for the 100% water
quality adjusted porewater concentration 105
Figure 3.2-24. Percent area (and 95% C.I.) of West Coast small estuaries vs. percent
successful embryonic development of Arbacia punctulata for the 50% water
quality adjusted porewater concentration 106
Figure 3.2-25. Percent area (and 95% C.I.) of West Coast small estuaries vs. percent
successful embryonic development of Arbacia punctulata for the 25% water
quality adjusted porewater concentration 107
Figure 3.3-1. Percent area (and 95% C.I.) of West Coast small estuaries
vs. benthic infaunal species richness 118
Figure 3.3-2. Percent area (and 95% C.I.) of West Coast small estuaries
vs. benthic infaunal H' diversity 119
Figure 3.3-3. Percent area (and 95% C.I.) of West Coast small estuaries
vs. benthic infaunal total abundance 120
XIII
-------
List of Tables
Table 2-1. West Coast sampling sites with station coordinates of locations sampled. 17
Table 2-2. Core environmental indicators for the EMAP Western Coastal survey. . . 25
Table 2-3. Environmental indicators under development or conducted
by collaborators during the EMAP Western Coastal survey 26
Table 2-4. Compounds analyzed in all three states in sediments and fish tissues. . . 37
Table 2-5. Summary of EMAP-Coastal chemistry sample collection,
preservation, and holding time requirements for sediment and fish tissues. . 38
Table 2-6. Methods used to analyze for contaminants in sediments and tissues. . . 39
Table 2-7. Units, method detection limits (MDL), and reporting limits (RL)
for sediment chemistry 44
Table 2-8. Units, method detection limits (MDL), and reporting limits (RL)
for tissue chemistry for compounds measured in all three states 46
Table 2-9. Summary of reference and matrix spike recoveries, and relative percent
differences (RPD) of duplicates 48
Table 2-10. Listing of primary and QA/QC taxonomists by taxon and region
for the 1999 Western Coastal EMAP study 51
Table 3.2-1. Summary statistics for sediment metal concentrations (ug/g)
for 190 stations from West Coast estuaries 79
Table 3.2-2. Mean sediment concentrations (ng/g dry weight) and frequency of
detection of the PAHs, PCBs and pesticides measured in all three states. . 93
Table 3.2-3. Species composition and relative abundance of the three
fish groups used in the tissue residue analysis 110
Table 3.2-4. Fish tissue residues of metals measured in all three states 111
Table 3.2-5. Fish tissue residues of total PCBs, total DDT and the
additional pesticides measured in all three states 113
Table 3.3-1. Summary statistics for benthic abundance, number of
species per benthic sample, and H' 121
xiv
-------
Table 3.3-2. Abundance, taxonomic grouping, and classification of the
ten most abundant benthic species in the three states including the
intensification sites in Northern California and Tillamook, Oregon 122
Table 3.3-3. Abundance, taxonomic grouping, and classification of the
ten most abundant benthic species in the three states excluding
the Northern California intensification stations 123
Table 3.3-4. Trawl duration and speed averaged across California, Oregon,
and Washington and in each individual state 125
Table 3.3-5. Mean number offish captured per trawl and mean number
offish species per trawl averaged across California, Oregon, and
Washington and for each individual state 126
Table 3.3-6. Ten numerically dominant fish species averaged across California,
Oregon, and Washington, including both the base and intensive stations. . 127
Table 3.3-7 Mean and standard deviation of the five most numerically abundant fish
species in California, Oregon, and Washington 128
xv
-------
Executive Summary
As a part of the National Coastal Assessment, the Environmental Monitoring and
Assessment Program (EMAP) initiated a five-year Western Coastal component in 1999.
The objectives of the program were: to assess the condition of estuarine resources of
Washington, Oregon and California based on a range of indicators of environmental
quality using an integrated survey design; to establish a baseline for evaluating how the
conditions of the estuarine resources of these states change with time; to develop and
validate improved methods for use in future coastal monitoring and assessment efforts
in the western coastal states; and to transfer the technical approaches and methods for
designing, conducting and analyzing data from probability based environmental
assessments to the states and tribes.
The focus of the study during 1999 was the small estuaries of Washington, Oregon, and
California, excluding Puget Sound, the main channel of the Columbia River, and San
Francisco Bay, which were sampled in 2000 during the second year of the program.
The environmental condition indicators used in this study included measures of: 1)
general habitat condition (depth, salinity, temperature, pH, total suspended solids,
sediment characteristics), 2) water quality indicators (chlorophyll a, nutrients), 3)
pollutant exposure indicators (dissolved oxygen concentration, sediment contaminants,
fish tissue contaminants, sediment toxicity), and 4) benthic condition indicators (diversity
and abundance of benthic infaunal and demersal fish species, fish pathological
anomalies).
The study utilized a stratified random sampling design, with the base study consisting of
150 sites equally divided among the three states. Additionally, intensification studies
were conducted that consisted of 30 sites located in Tillamook Bay, Oregon, and 30
sites distributed among the mouths of river dominated estuaries in northern California.
All sites were combined for statistical analysis. Cumulative distribution functions (CDFs)
were produced using appropriate sampling area weightings to represent the areal extent
associated with given values of an indicator variable for the small estuaries of the West
Coast.
Reflecting the fact that the sampling effort spanned both the Columbian and Californian
Biogeographic Provinces, the indicators of general habitat condition showed wide
ranges of values, e.g., bottom water temperatures from 8.5 to 32.1 °C. Approximately
54% of the area of the small West Coast estuaries would be classified as euhaline (>30
psu) based on the EMAP sampling. Approximately 65% of the estuarine area had
sandy sediments (<20% silt clay), 29% had intermediate muddy sands (20-80% silt
clay), and 6 % had mud sediments (>80% silt clay). The TOC content of sediments was
< 1% in approximately 84% of the area of the small West Coast estuaries.
The pH of bottom waters for the small estuaries of West Coast states had the
surprisingly wide range of from 5.1 to 10.2, with extreme values associated with low
salinity locations. There was no geographic pattern to high values of chlorophyll a.
xvi
-------
Most water quality indicators showed similar CDF patterns, with high values being
observed in a very small percentage of estuarine area, thus generating extensive right
hand tails to CDF distributions. For example, the average water column concentration of
nitrate/nitrite of small West Coast estuaries ranged from 0 to 3472 ug L"1, but only 2.7 %
of estuarine area had nitrate/nitrite values that exceeded concentrations of 300 ugl_"1.
Approximately 75% of estuarine area had molar ratios of average water column total
nitrogen to total phosphorus (N/P) values < 16, suggesting nitrogen limitation. While
total suspended solids (TSS) ranged from 0 to 276.2 mg L"1, approximately 95% of
estuarine area had TSS < 19.1 mg L"1. Only about 12 % of estuarine area showed an
indication of strong water column stratification as indicated by the difference in surface
and bottom salinities, suggesting the estuarine areas sampled are generally well mixed.
Among pollution exposure indicators, less than four percent of estuarine area had
dissolved oxygen concentrations in bottom waters below 5 mg/L. High values of
potentially toxic metals generally occurred in a very small percentage of the estuarine
area sampled, with maximum values of many of the metals being observed in the highly
urbanized Los Angeles Harbor (cadmium, copper, lead, selenium, silver, tin, zinc). DDT
and other pesticides were detected in a relatively small percentage of estuarine area.
Seventy- three percent of estuarine area had non-detectable levels of total PCBs.
Highest levels of organic contaminants (pesticides, PAHs) generally were associated
with urbanized estuaries of southern California.
Sediment toxicity tests with the amphipod Ampelisca abdita had control-corrected
survivorship < 80 % in only about 9 % of estuarine area. Using sediment pore water
bioassays, the control corrected, percent fertilization of eggs of the sea urchin Arbacia
punctulata was < 91 % in only about 10.5 % of estuarine area for the 100% of the water
quality adjusted (WQA) porewater treatment. Survivorship was higher for both 50% and
25% WQA porewater treatments. For a similar test using percent successful
development of Arbacia punctulata embryos, the control-corrected normal development
of embryos was < 91 % in about 49 % of area of small West Coast estuaries for the
100% of the WQA porewater treatment. Normal embryo development was higher for
both 50% and 25% WQA porewater treatments.
There was a total of 144 successful trawls across the three states, but due to the
number of stations without successful trawls, the analysis of the fish trawl data is limited
to summary statistics and species composition, and no CDFs are presented. The
number of individuals per trawl averaged 33.7 fish per trawl, with a low of 13.9 in
Oregon and a high of 68.0 in California. Species richness averaged 3.53 fish species
per trawl, with a low of 2.63 in Oregon and a high of 5.46 in California. A report on the
frequency offish pathologies will be produced separately by NOAA.
Obtaining the target organisms (flatfish) for tissue analysis of contaminants proved
difficult, and tissue analyses were conducted on only 53% of the total stations occupied.
Thus cumulative distribution functions were not computed. There was no consistent
spatial pattern in location of maximum fish tissue metal concentrations, with highest
xvii
-------
values of mercury being recorded in several California estuaries, highest arsenic and
lead values being recorded in several Washington estuaries, and highest copper values
being recorded in an Oregon estuary. Maximum fish tissue residues for total PCBs
were associated with urbanized estuaries in California, which were also associated with
highest sediment concentrations of these contaminants. Tissue residues of DDT and its
metabolites were considerably higher than other pesticides measured.
A total of 187 samples of benthic infauna (>1 mm) were obtained using either grabs or a
combination of smaller corers to obtain equivalent surface area (0.1 m2). Reflecting the
wide geographic distribution of sampling, a total of 841 non-colonial benthic taxa were
recorded. Species richness ranged from 1 to 157 taxa per sample. Lowest species
richness tended to be associated with low salinity sites, and highest species richness
was associated with salinities > 30 psu. About 50% of the area of small West Coast
estuaries had species richness < 17 species per sample. The northern California
intensive study sites tended to have lower species richness and H' diversity values than
other stations.
Benthic infaunal abundance averaged 1378.9 individuals per sample, with lowest mean
abundance per sample in Washington estuaries and highest mean abundance values in
California estuaries, particularly the northern California intensive study sites. About
50% of the area of small West Coast estuaries had mean infaunal abundance < 151
individuals per sample. Two amphipod species (Americorophium spinicorne,
Americorophium salmonis), which had extremely high abundances in several northern
California locations, made up 54 % of total infaunal abundance in the study. Among the
10 most abundant taxa at all study sites, nonindigenous and cryptogenic (species of
uncertain geographic origin) species made up 6 % of total infaunal abundance.
The 1999 Western Coastal EMAP study provides the first quantitative assessment of
the condition of the small estuaries of Washington, Oregon and California. When these
data are combined with the data collected in 2000 from the three largest estuarine
systems on the West Coast (Puget Sound, Columbia River, San Francisco Bay), there
will exist the first comprehensive data set for evaluating the overall condition of all
estuarine systems of the West Coast.
XVIII
-------
1.0 Introduction
1.1 Program Background
Safeguarding the natural environment is fundamental to the mission of the US
Environmental Protection Agency (EPA). The legislative mandate to undertake this part
of the Agency's mission is embodied, in part, in the Clean Water Act (CWA). Sections of
this Act require the states to report the condition of their aquatic resources and list those
not meeting their designated use (Sections 305b and 303d, respectively). Calls for
improvements in environmental monitoring date back to the late 1970's, and have been
recently reiterated by the General Accounting Office (GAO, 2000). The GAO report
shows that problems with monitoring of aquatic resources continue to limit states'
abilities to carry out several key management and regulatory activities on water quality.
At the national level, there is a clear need for coordinated monitoring of the nation's
ecological resources. As a response to these needs at state and national levels, the
EPA Office of Research and Development (ORD) has undertaken research to support
the Agency's Regional Offices and the states in their efforts to meet the CWA reporting
requirements. The Environmental Monitoring and Assessment Program (EMAP) is one
of the key components of that research and EMAP-West is the newest regional
research effort in EMAP. From 1999 through 2005, EMAP-West will seek to develop
and demonstrate the tools needed to measure ecological condition of the aquatic
resources in the 14 western states in EPA's Regions 8,9, and 10.
The Coastal Component of EMAP-West is a partnership with the states of California,
Oregon and Washington, the National Oceanic and Atmospheric Administration, and the
Biomonitoring of Environmental Status and Trends Program (BEST) of the U.S.
Geological Survey, to measure the condition of the estuaries of these three states.
Sampling began during the summer of 1999 and the initial phase of estuarine sampling
was completed in 2000. Data from this program will be the basis for individual reports of
condition for each state, and will be used to provide data to the National Coastal
Assessment.
The US EPA's National Coastal Assessment (NCA) is a five-year effort led by EPA's
Office of Research and Development to evaluate the assessment methods it has
developed to advance the science of ecosystem condition monitoring. This program will
survey the condition of the Nation's coastal resources (estuaries and offshore waters)
by creating an integrated, comprehensive coastal monitoring program among the
coastal states to assess coastal ecological condition. The NCA is accomplished
through strategic partnerships with all 24 U.S. coastal states. Using a compatible,
probabilistic design and a common set of survey indicators, each state conducts the
survey and assesses the condition of its coastal resources independently. Because of
the compatible design, these state estimates can be aggregated to assess conditions at
the EPA Regional, biogeographical, and national levels.
-------
This report provides a statistical summary of the data from the first year of sampling
(1999) for the small estuarine systems of the states of Washington, Oregon, and
California (excluding Puget Sound, the main channel of the Columbia River, and San
Francisco Bay).
1.2 The Western United States Context for a Coastal Condition Assessment
Nationwide, growth of the human population is disproportionally concentrated in the
coastal zone (Culliton et al., 1990). Within the coastal region of the western U.S.,
greatest population expansion has been in the major urban areas of Seattle, Portland,
the San Francisco Bay area, and much of Southern California. These metro areas are
either directly located on coastal water bodies or, like Portland, are on major rivers and
thus influence the estuaries downstream. While development around the estuaries
between north Puget Sound and Point Reyes, CA, has been less intense, substantial
population growth is taking place across the region. Human population growth in the
coastal zone of the west is a principal driver for many ecological stressors such as
habitat loss, pollution, and nutrient enhancement which alter coastal ecosystems and
affect the sustainability of coastal ecological resources (Copping and Bryant, 1993).
Increased globalization of the economy is a major driver influencing the introduction of
exotic species into ports and harbors. Major environmental policy decisions at local,
state and federal levels related to land use planning, growth management, habitat
restoration and resource utilization will determine the future trajectory for estuarine
conditions of the western U.S.
Changes associated with human population growth in the western coastal region tend to
be most obvious in the larger, urban areas, but all coastal resources have been
subjected to significant alterations over the last 150 years. In one of the earliest
ecological alterations, sea otters, a known ecological keystone species (Simenstad et
al., 1978), were largely removed from western coastal ecosystems by 1810, and
populations have never recovered. The wave of western mining in the late 1800's had
limited effects on most coastal systems in terms of altering estuaries or causing
chemical pollution (Burning, 1996). Outside of the major ports, western estuaries are
believed to have generally low concentrations of toxic pollutants because of relatively
low population densities and low levels of heavy industry (Copping and Bryant, 1993),
but data for most estuaries are sparse.
Due to exploitative fishing in the Pacific Northwest, native oyster populations were
largely wiped out by the late 1800's, and salmon catch peaked by the early 1900's
(Burning, 1996). Resource exploitation for agriculture, logging and damming each
resulted in massive changes to land use practices throughout the region. In the
Chesapeake Bay region, deforestation associated with human settlement and
agricultural clearing was shown to have led to a 100% increase in sediment
accumulation rates (Cooper and Brush, 1991) during the 1800's. Sedimentation
problems associated with land use changes may be especially acute along the West
Coast north of San Francisco due to the combination of steep coastal watersheds, high
-------
rainfall, and timber harvesting. Nutrient and sediment loadings from population centers
will augment the increased flux of these materials resulting from the larger scale
watershed alterations associated with logging of the coastal mountains (Howarth et al.,
1991).
The increase in regional and international marine commerce along the West Coast has
resulted in the introduction of nonindigenous species. The effect of nonindigenous
species on estuarine habitats has only recently come under scrutiny (Carlton and
Geller, 1993), but the potential for ecological transformation is great. Some 367 marine
invertebrate taxa were recorded in the ballast water of ships arriving in Coos Bay,
Oregon, from Japan (Carlton and Geller, 1993). In Washington state, the introduction of
smooth cordgrass, Spartina alterniflora, has resulted in the conversion of hundreds of
hectares of mud flat to salt marsh habitat with consequences to the ecosystem that
have not yet been fully defined (Simenstad and Thorn, 1995).
Benthic environments are areas where many types of impacts from the stressors
described above will tend to accumulate. Deposition of toxic materials, accumulation of
sediment organics, and oxygen deficiency of bottom waters typically have a greater
impact on benthic organisms than on planktonic and nektonic organisms because of
their more sedentary nature. Long-term studies of the macrobenthos (Reish, 1986;
Holland and Shaughnessey, 1986) demonstrate that macrobenthos are a sensitive
indicator of pollutant effects. Benthic assemblages are also closely linked to both lower
and higher trophic levels, as well as to processes influencing water and sediment
quality, and therefore appear to integrate responses of the entire estuarine system
(Leppakoski, 1979; Holland and Shaughnessey, 1986).
Biologically, the EMAP Western Coastal study area is represented by two biogeographic
provinces, the Columbian Province, which extends from the Washington border with
Canada to Point Conception, California, and the Californian Province, which extends
from Point Conception to the Mexican border. Within the biogeographic provinces there
are also major transitions in the distribution of the human population. Major population
centers occur in the southern end of Puget Sound, around San Francisco Bay, and
generally surrounding most of the estuaries of southern California. In contrast, the
region of coastline from north of San Francisco Bay through northern Puget Sound has
a much lower population density. While it may be presumed that the magnitude of
anthropogenic impacts will tend to show a similar distribution, this hypothesis has not
yet been tested for West Coast estuaries.
1.3 Objectives
The EMAP sampling program conducted in the small estuaries of the West Coast in
1999 was the first-year component of the larger EMAP Western Coastal Program, which
has the following objectives:
-------
1. To assess the condition of estuarine resources of Washington, Oregon and California
based on a range of indicators of environmental quality using an integrated survey
design;
2. To establish a baseline for evaluating how the conditions of the estuarine resources
of these states change with time;
3. To develop and validate improved methods for use in future coastal monitoring and
assessment efforts in the western coastal states;
4. To transfer the technical approaches and methods for designing, conducting and
analyzing data from probability based environmental assessments to the states and
tribes.
-------
2.0 Methods
2.1 Sampling Design and Statistical Analysis Methods
2.1.1 Background
The EMAP approach to evaluating the condition of ecological resources is described in
reports such as Diaz-Ramos et al. (1996), Stevens (1997), Stevens and Olsen (1999),
and is also presented in summaries provided on the internet at the URL:
http://www.epa.gov/nheerl/arm/index.htm
A brief summary from these documents follows.
Given that it is generally impossible to completely census an extensive resource such
as the set of all estuaries on the West Coast, a more practical approach to evaluating
resource condition is to sample selected portions of the resource using probability
based sampling. Studies based on random samples of the resource rather than on a
complete census are termed sample surveys. Sample surveys offer the advantages of
being affordable, and of allowing extrapolations to be made of the overall condition of
the resource based on the random samples collected. Survey methods are widely used
in national programs such as forest inventories, agricultural statistics survey, national
resource inventory, consumer price index, labor surveys, and such activities as voter
opinion surveys.
A survey design provides the approach to selecting samples in such a way that they
provide valid estimates for the entire resource of interest. Designing and executing a
sample survey involves five steps: (1) creating a list of all units of the target population
from which to select the sample, (2) selecting a random sample of units from this list, (3)
collecting data from the selected units, (4) summarizing the data with statistical analysis
procedures appropriate for the survey design, and (5) communicating the results. The
list or map that identifies every unit within the population of interest is termed the
sampling frame.
The sampling frame for the EMAP Western Coastal Program was developed from
USGS 1:100,000-scale digital line graphs and stored as a CIS data layer in the
ARC/INFO program. A series of programs and scripts (Bourgeois et al., 1998) was
written to create a random sampling generator (RSG) that runs in ArcView. Site
selection consisted of using the RSG to first overlay a user-defined sampling grid of
hexagons over the spatial resource which consisted of all estuaries of the West Coast.
The area of the hexagons was controlled by adjusting the distance to hexagon centers,
and by defining how many sample stations were to be generated for each sampling
region. After the sampling grid was overlaid on the estuarine resource, the program
randomly selected hexagons and randomly located a sampling point within the hexagon.
Only one sampling site was selected from any hexagon selected. The program
-------
determined whether a sampling point fell in water or on land, and sites that fell on land
were not included. The RSG was run iteratively until a hexagon size was determined
which generated the desired number of sampling sites within the resource (Bourgeois et
al., 1998).
Hexagon size may be different for classes of estuarine systems of different areal extent.
The final data analysis which provides the estimates of resource condition then weights
the samples based on the area of the estuarine class. Stevens (1997) terms this a
random tessellation stratified survey design applied to each estuarine resource class.
2.1.2 Sampling Design
2.1.2.1 1999 West Coast Design
The assessment of condition of small estuaries conducted in 1999 was the first phase of
a planned two-year comprehensive assessment of all estuaries of the states of
Washington, Oregon and California. The complete assessment will require the
integrated analysis of data collected from the smaller estuarine systems in 1999 and the
larger estuarine systems in 2000. The intent of the design is to be able to combine data
from all stations for analysis, using the inclusion probabilities, defined as the total
estuarine area in km2 within a given design stratum (= estuarine size class), to weight
the representation of samples in the combined analysis.
The West Coast sampling frame was constructed as a CIS coverage that would include
the total area of the estuarine resource of interest. Available CIS coverages were not
perfect representations of the estuarine resource, and so the coverages were defined to
ensure that they included the resource, but may have possibly included some nearby
land or inland water. The inland boundary of the sampling frame was defined as the
head of salt water influence, while the seaward boundary was defined by the confluence
with the ocean. Sample locations could fall within any water depth contained within the
estuarine resource which was bounded by the shoreline. In some cases, extremely
shallow sites were deemed inaccessible by field crews with the sampling gear specified
(Section 2.6). Emergent salt marsh areas were not included in the sampling frame
because the required indicators to deal with marsh habitats were not available.
For the state of Washington, the 1999 design included only estuaries along the
coastline outside of the Puget Sound system, and consisted of a total of 50 sites (Table
2.1). Tributary estuaries of the Columbia River located within Washington state were
included in the 1999 sampling effort, while the main channel area was not sampled until
2000 (as part of the 2000 Oregon design). The sampling frame used three hexagonal
grid sizes to cover the size range of estuaries: 0.86, 7.79, 36.58 km2. The hexagonal
grid sizes were used to locate random sample sites within a total of four strata
representing differing total areas of the estuarine resource in Washington (Table 2.1).
To insure some level of sampling across the entire range of estuarine sizes, sampling
effort was partitioned as 10 stations within the smallest estuarine size class, 25 stations
-------
within the two strata representing the medium sized estuaries, and 15 stations in the
largest size class. No alternate or oversample sites were included in the design.
The Oregon 1999 design included only small estuaries of the state and consisted of 50
sites. Tributary estuaries of the Columbia River located within Oregon were included in
the 1999 sampling effort, while the main channel area was not sampled until 2000. The
sampling frame for small estuaries utilized four hex sizes to cover the size range of
estuaries: 1.24, 3.46, 4.58, and 7.28 km2. Approximately equal sampling effort was
placed in each of the four estuarine strata, which represented differing size classes of
estuaries, to insure some level of sampling across the entire range of estuarine sizes.
An intensive sampling effort was also designed for Tillamook Bay, where a total of 30
sites were selected using a hex size of 1.04 km2. No points from the base study design
were placed in Tillamook Bay. All sites from both the base study and intensive study
were combined for analysis. No alternate or oversample sites were included in the
design.
The 1999 California base study design included all estuaries of the state with the
exception of San Francisco Bay, and consisted of a total of 50 sites. The sampling
frame utilized three hexagonal grid sizes to cover the size range of estuaries in the
sampling frame: 0.86, 7.79, and 12.50 km2. Approximately equal sampling effort was
placed in each of the three estuarine size classes (<5, 5-25 and >25 km2) to ensure
some level of sampling across the entire range of estuarine sizes. No alternate or
oversample sites were selected during the design, and thus any sites which could not
be sampled were not replaced.
The estuarine systems on the northern California coast, with the exception of the Arcata
and Humboldt Bay systems, are relatively poorly studied. A number of the rivers which
discharge directly into the Pacific Ocean have been listed as failing to meet designated
uses and have been designated for development of Total Maximum Daily Loadings
(TMDL). At the request of the Region 9 Office of EPA, an intensive study was
conducted to sample the river mouth estuaries of both TMDL listed and non-TMDL
listed systems of Northern California. The purpose of this assessment was to determine
if there was any difference in the estimates of condition for the two categories of
estuarine resource.
Using finer scale hexagonal grids, 30 sites were randomly selected at the mouths of the
river systems in Northern California. The design for this intensive study incorporated 6
differing hexagonal grid sizes: 0.0346, 0.0498, 0.0585, 0.0800, 0.0914, and 0.1060 km2.
The hexagonal grid sizes were used to locate random sample sites within a total of
seven strata representing differing total areas of the estuarine resource in these
Northern California river mouth systems (Table 2-1). Sample sites were divided equally
between streams with and without TMDL listings (Table 2-1). No alternate or
oversample sites were selected during the design, and thus any sites which could not
be sampled were not replaced.
-------
While the intent of the California design was to be able to integrate all study sites
seamlessly into combined analyses, an inadvertent design change occurred which
somewhat complicates interpretation of results. In defining the target population for the
Northern California sites, a restriction of sampling to a distance of 0.25 km from the
estuarine mouth was imposed. This definition differs from that of the remainder of the
West Coast assessment which used a target population defined by the head of salt in
the estuary. In order to prevent duplicative sampling effort, the intensive study of
northern California small river systems had been excluded from the frame for the base
California study. Thus, a small area (approximately 10 km2) representing the portion of
the Northern California river systems excluded from the intensive study was
inadvertently omitted from the California sampling frame.
2.1.2.2 2000 West Coast Design
While results of the 2000 sampling effort are not presented in this report, a description
of the sample design for 2000 is provided in order to demonstrate the overall plan for
the western coastal assessment effort.
The Washington 2000 sampling design included only the large "estuary" of Puget
Sound and its tributaries. Site selection for this estuary used a combined approach in
order to allow collaboration with a survey previously conducted by NOAA under the
NOAA National Status and Trends Program. The overall design combined the existing
NOAA probability based, randomized monitoring design with the EMAP Western
Coastal study design. The EMAP hexagonal grid was extended to include Canadian
waters at the north end of Puget Sound, and then was overlaid on the existing NOAA
monitoring sites. If a NOAA site fell within a hexagon, the site was designated as the
EMAP sampling point. If not, a random site was selected based on the EMAP
protocols. The design incorporated three different hex sizes, two covering most of the
Puget Sound region (86.6, 250.28 km2), and one used for intensifying in the region of
the San Juan Islands (21.65 km2). There were 41 stations selected based on the NOAA
sampling stations, in addition to 30 new EMAP stations, of which 10 were associated
with the San Juan Islands. No alternate or oversampling sites were included in the
design frame.
The Oregon 2000 design included only the main channel area of Columbia River. The
Columbia River system was split into two subpopulations, the lower, saline portion and
the upper, freshwater portion, with hex sizes of 13.85 and 5.4 km2 and total numbers of
stations of 20 and 30, respectively. No alternate or oversample sites were included in
the design.
The 2000 California design included only San Francisco Bay and its tributaries. Site
selection for this estuary used a combined approach in order to allow collaboration with
a survey being conducted by NOAA under the NOAA National Status and Trends
Program. An EMAP sampling design was developed specifically for NOAA to implement
a multiyear monitoring program to characterize condition of the small systems within the
8
-------
San Francisco Bay. To insure complete coverage of the bay for the EMAP Western
Coastal study, the NOAA design was augmented with a sampling design which split the
Bay into two subpopulations (open bay and smaller surrounding systems). For the open
bay, a hex size of 36.58 km2 was used and 31 sites were generated. For the smaller
systems, a different hexagon size (3.46 km2) was used to generate 19 sites for
sampling. This grid was overlaid on the newly designed NOAA small systems
monitoring project. If a NOAA site fell within a hexagon, the site was used as the
sampling point. If not, a random point was generated based on the standard
randomization routines used by Western Coastal EMAP as part of the National Coastal
Assessment. No alternate or oversample sites were selected.
-------
MAKAHBAY
OZETTE
RIVER
I +
^
HOKO RIVER
a
DUNGENESS BAY
FRESHWATER BAY mcrnvirBV BAV
9» • DISCOVERY BAY
1*
WASHINGTON
KALALOCH CREEK®
v
RAFT RIVER «
QUINAULT RIVER
a
-5t +
CONNER CREEK
GRAYS HARBOR
WILLAPA BAY
COLUMBIA RIVER ESTUARIES
(WASHINGTON)
-I +
.125'
\
.124"
Base Study Sites a Abandoned Sites
50 0 SO 100 ISO km
Figure 2-1. Location of Washington EMAP survey sites.
10
-------
uK
COLUMBIA RIVER ESTUARIES
(OREGON)
WASHINGTON
NEHALEM RIVER
TILLAMOOKBAY
TILLAMOOK RIVER
NETARTS BAY
NESTUCCA RTVER
LITTLE NESTUCCA RIVER
SALMON RIVER
SILETZBAY®
YAQUWABAY %
YAQUINA RIVER
ALSEA RTVER •
YACHATS RIVER $b_
ROCK CREEK 8
OREGON
Intensive Study Sites
50
Base Study Sites
0 50
Abandoned Sites
700 km
Figure 2-2. Location of EMAP survey sites along the northern portion of the Oregon
coast, including survey sites for the intensification study of Tillamook Bay.
11
-------
SIUSLAW RIVER
SMITH RIVER
UMPQUA RIVER
COOS BAY
SOUTH SLOUGH 4
COOS RIVER
CATCHING SLOUGH
ROGUE RIVER
OREGON
CALIFORNIA
-124<
-123'
Base Study Sites
so
100 km
Figure 2-3. Location of EMAP survey sites along the southern portion of the Oregon
coast.
12
-------
TILIAMOOK BAY
.124009'
I
Intensive Study Sites
10 km
Figure 2-4. Location of EMAP survey sites for the intensification study of Tillamook
Bay, Oregon.
13
-------
SMITH RIVER (CA)
WILSON CREEK ft
KLAMATH RIVER
BIG LAGOON
LITTLE RTVER •
ARCATABAY 0
HUMBOLDTBAY A
EEL RIVER •
BEAR RTVER •
t
NOYO RIVER
CASPAR CREEK
BIG RIVER
ALBION RIVER '
ELK CREEK
GARCIA RIVER
I
OREGON
CALIFORNIA
.122"
I
50
Intensive Study Sites « Base Study Sites
0 50 100 150 200km
Figure 2-5. Location of California EMAP survey sites in Northern California from the
Oregon border to the Garcia River.
14
-------
RUSSIAN RIVER
TOMALES
BAY
ESTERO AMERICANO
ESTERO SAN ANTONIO
9
DRAKES BAY
SANTA CRUZ HARBOR
PAJARO RIVER
MONTEREY HARBOR
CARMEL BAY
X.
s
s
CALIFORNIA
SANTA YNEZ RIVER
-1^0° 9
• Intensive Study Sites $ Base Study Sites
700 0 700 200 km
Figure 2-6. Location of California EMAP survey sites in Northern and Central California
from the Russian River to the Santa Ynez River.
15
-------
CALIFORNIA
SANTA BARBARA ®
HARBOR VENTURA RIVER
® ~
CHANNEL ISLANDS HARBOR
POINT MUGC
LAGOON
KING HARBOR* *,_ LOS ANGELES RIVER
LOS ANGELES HARBOR
LONG BEACH HARBOR
DANA POINT 9
HARBOR
SANTA MARGARITA RIVER'
AGUA HEDIONDA CREEK
SAN DIEGO RIVER ^
SAN DIEGO BAY
ns +0 IS/V^IA IVlAKtjAKI I A KIV h.K —
"I **5->. A
-1U" -117"
9 Base Study Sites
700 0 700 200 km
Figure 2-7. Location of California EMAP survey sites in Central and Southern California
from Santa Barbara to the Mexican border.
16
-------
Table 2-1. West Coast sampling sites with station coordinates of locations sampled.
The northern California small estuary TMDL study sites are noted as either Y = TMDL
Site, N = Non-TMDL Site. Frame area represents the total estuarine area within a
stratum. An * in a station location indicates the site was abandoned prior to sampling.
EMAP Sta. No. Latitude Longitude Estuary
WA99-0001
WA99-0002
WA99-0003
WA99-0004
WA99-0005
WA99-0006
WA99-0007
WA99-0008
WA99-0009
WA99-0010
WA99-001 1
WA99-0012
WA99-0013
WA99-0014
WA99-0015
WA99-0016
WA99-0017
WA99-0018
WA99-0019
WA99-0020
WA99-0021
WA99-0022
WA99-0023
WA99-0024
WA99-0025
WA99-0026
WA99-0027
WA99-0028
WA99-0029
WA99-0030
WA99-0031
WA99-0032
WA99-0033
WA99-0034
WA99-0035
WA99-0036
WA99-0037
WA99-0038
WA99-0039
WA99-0040
WA99-0041
WA99-0042
WA99-0043
WA99-0044
WA99-0045
WA99-0046
WA99-0047
WA99-0048
WA99-0049
WA99-0050
OR99-0001
OR99-0002
OR99-0003
OR99-0004
OR99-0005
OR99-0006
OR99-0007
OR99-0008
OR99-0009
48.320
48.314
48.305
48.288
48.181
48.149
48.148
48.143
48.160
48.079
48.058
48.021
48.003
47.997
47.606
47.463
47.347
*
47.089
47.004
47.005
46.966
46.940
46.935
46.967
46.921
46.873
46.870
46.848
46.715
46.704
*
46.650
46.567
46.539
46.418
*
46.310
46.301
46.273
*
46.263
46.302
46.300
46.295
46.287
46.275
46.095
46.085
45.947
46.188
46.21 1
46.180
46.217
46.167
46.208
46.169
46.226
46.190
-124.680
-124.670
-124.671
-124.365
-124.708
-123.633
-123.601
-123.616
-123.148
-122.900
-122.905
-122.859
-122.843
-122.874
-124.373
-124.339
-124.298
*
-124.176
-124.040
-124.000
-123.951
-124.104
-124.028
-123.858
-124.067
-124.034
-124.022
-124.032
-124.045
-123.887
*
-124.012
-123.942
-123.924
-123.418
*
-124.009
-124.026
-123.973
*
-123.998
-123.711
-123.698
-123.703
-123.727
-123.717
-122.922
-122.880
-122.786
-123.912
-123.724
-123.865
-123.672
-123.893
-123.688
-123.872
-123.588
-123.744
Makah Bay
Makah Bay
Makah Bay
Hoko River
Ozette River
Freshwater Bay
Freshwater Bay
Freshwater Bay
Dungeness Bay
Discovery Bay
Discovery Bay
Discovery Bay
Discovery Bay
Discovery Bay
KalalochCreek
Raft River
Quinault River
Quinault River
Conner Creek
Grays Harbor
Grass Creek
Grays Harbor
Grays Harbor
Grays Harbor
Grays Harbor
Grays Harbor
Beardslee Slough
Beardslee Slough
Grays Harbor
Willapa Bay
Willapa Bay
Willapa Bay
Willapa Bay
Willapa Bay
Willapa Bay
Willapa Bay
Willapa Bay
Baker Bay
Baker Bay
Baker Bay
Grays River
Baker Bay
Grays Bay
Grays Bay
Grays Bay
Grays Bay
Grays Bay
Cowlitz River
Carrolls Channel
Martin Slough
Youngs Bay
Cathlamet Bay
Youngs Bay
Cathlamet Bay
Youngs Bay
Cathlamet Bay
Youngs Bay
Marsh Island Creek
Cathlamet Bay
Hex Frame Area
Size
7.79
7.79
7.79
0.86
0.86
7.79
7.79
7.79
7.79
7.79
7.79
7.79
7.79
7.79
0.86
0.86
7.79
7.79
0.86
36.58
0.86
36.58
36.58
36.58
36.58
36.58
0.86
0.86
36.58
36.58
36.58
36.58
36.58
36.58
36.58
36.58
36.58
7.79
7.79
7.79
0.86
7.79
7.79
7.79
7.79
7.79
7.79
7.79
7.79
0.86
3.46
3.46
3.46
3.46
3.46
3.46
3.46
1.24
3.46
km2
77.288
77.288
77.288
8.363
8.363
77.288
77.288
77.288
1 1 1 .478
1 1 1 .478
1 1 1 .478
1 1 1 .478
1 1 1 .478
1 1 1 .478
8.363
8.363
77.288
77.288
8.363
562.230
8.363
562.230
562.230
562.230
562.230
562.230
8.363
8.363
562.230
562.230
562.230
562.230
562.230
562.230
562.230
562.230
562.230
1 1 1 .478
1 1 1 .478
1 1 1 .478
8.363
1 1 1 .478
1 1 1 .478
1 1 1 .478
1 1 1 .478
1 1 1 .478
1 1 1 .478
77.288
77.288
8.363
43.192
43.192
43.192
43.192
43.192
43.192
43.192
13.578
43.192
Stratum
WA99-002
WA99-002
WA99-002
WA99-001
WA99-001
WA99-002
WA99-002
WA99-002
WA99-003
WA99-003
WA99-003
WA99-003
WA99-003
WA99-003
WA99-001
WA99-001
WA99-002
WA99-002
WA99-001
WA99-004
WA99-001
WA99-004
WA99-004
WA99-004
WA99-004
WA99-004
WA99-001
WA99-001
WA99-004
WA99-004
WA99-004
WA99-004
WA99-004
WA99-004
WA99-004
WA99-004
WA99-004
WA99-003
WA99-003
WA99-003
WA99-001
WA99-003
WA99-003
WA99-003
WA99-003
WA99-003
WA99-003
WA99-002
WA99-002
WA99-001
OR99-003
OR99-003
OR99-003
OR99-003
OR99-003
OR99-003
OR99-003
OR99-001
OR99-003
TM[
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
17
Table continued on next page
-------
OR99-0010
OR99-001 1
OR99-0012
OR99-0013
OR99-0014
OR99-0015
OR99-0016
OR99-0017
OR99-0018
OR99-0019
OR99-0020
OR99-0021
OR99-0022
OR99-0023
OR99-0024
OR99-0025
OR99-0026
OR99-0027
OR99-0028
OR99-0029
OR99-0030
OR99-0031
OR99-0032
OR99-0033
OR99-0034
OR99-0035
OR99-0036
OR99-0037
OR99-0038
OR99-0039
OR99-0040
OR99-0041
OR99-0042
OR99-0043
OR99-0044
OR99-0045
OR99-0046
OR99-0047
OR99-0048
OR99-0049
OR99-0050
OR99-0051
OR99-0052
OR99-0053
OR99-0054
OR99-0055
OR99-0056
OR99-0057
OR99-0058
OR99-0059
OR99-0060
OR99-0061
OR99-0062
OR99-0063
OR99-0064
OR99-0065
OR99-0066
OR99-0067
OR99-0068
OR99-0069
OR99-0070
OR99-0071
OR99-0072
OR99-0073
OR99-0074
OR99-0075
OR99-0076
OR99-0077
OR99-0078
OR99-0079
OR99-0080
46.189
46.186
46.149
46.187
46.170
46.134
46.129
46.123
45.691
45.394
45.197
45.166
45.040
44.925
44.622
44.599
44.574
44.41 4
44.305
44.188
44.01 1
44.022
44.740
43.762
43.725
44.772
43.722
43.693
43.692
43.423
43.414
43.406
43.386
43.404
43.368
43.341
43.370
43.377
43.350
43.321
42.423
45.552
45.547
45.551
45.534
45.539
45.536
45.538
45.528
45.531
45.524
45.517
45.524
45.51 1
45.517
45.509
45.515
45.503
45.509
45.51 1
45.498
45.506
45.498
45.497
45.491
45.501
45.495
45.491
45.481
45.468
45.441
-123.746
-123.681
-123.817
-123.592
-123.144
-123.272
-123.226
-123.036
-123.899
-123.953
-123.961
-123.944
-123.994
-124.018
-124.034
-124.016
-123.963
-123.999
-124.115
-124.036
-124.126
-123.881
-124.136
-124.005
-124.146
-123.903
-124.124
-124.100
-124.065
-124.246
-124.207
-124.218
-124.292
-124.199
-124.304
-124.320
-124.148
-124.108
-124.169
-124.154
-124.419
-123.929
-123.935
-123.912
-123.935
-123.923
-123.932
-123.906
-123.929
-123.912
-123.929
-123.934
-123.912
-123.921
-123.891
-123.933
-123.901
-123.933
-123.911
-123.891
-123.887
-123.895
-123.908
-123.891
-123.894
-123.869
-123.894
-123.900
-123.900
-123.885
-123.877
Cathlamet Bay
Cathlamet Bay
Youngs River
Knappa Slough
Bradbury Slough
Wallace Slough
Clatskanie River
Rinearson Slough
Nehalem River
Netarts Bay
Nestucca River
Little Nestucca River
Salmon River
Siletz Bay
Yaquina Bay
Yaquina River
Yaquina River
Alsea River
Yachats River
Rock Creek
Siuslaw River
Siuslaw River
Umpqua River
Smith River (OR)
Umpqua River
Smith River (OR)
Umpqua River
Scholfield Creek
Umpqua River
Coos Bay
Coos Bay
Coos Bay
Coos Bay
Coos Bay
Coos Bay
South Slough
Coos River
Coos River
Catching Slough
Catching Slough
Rogue River
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook Bay
Tillamook River
3.46
3.46
7.28
1.24
7.28
7.28
1.24
1.24
7.28
7.28
1.24
1.24
1.24
7.28
7.28
7.28
7.28
1.24
1.24
1.24
7.28
7.28
4.58
7.28
4.58
7.28
4.58
1.24
4.58
4.58
4.58
4.58
4.58
4.58
4.58
7.28
1.24
1.24
1.24
1.24
7.28
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
1.04
43.192
43.192
99.605
13.578
99.605
99.605
13.578
13.578
99.605
99.605
13.578
13.578
13.578
99.605
99.605
99.605
99.605
13.578
13.578
13.578
99.605
99.605
59.163
99.605
59.163
99.605
59.163
13.578
59.163
59.163
59.163
59.163
59.163
59.163
59.163
99.605
13.578
13.578
13.578
13.578
99.605
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
33.732
OR99-003
OR99-003
OR99-002
OR99-001
OR99-002
OR99-002
OR99-001
OR99-001
OR99-002
OR99-002
OR99-001
OR99-001
OR99-001
OR99-002
OR99-002
OR99-002
OR99-002
OR99-001
OR99-001
OR99-001
OR99-002
OR99-002
OR99-004
OR99-002
OR99-004
OR99-002
OR99-004
OR99-001
OR99-004
OR99-004
OR99-004
OR99-004
OR99-004
OR99-004
OR99-004
OR99-002
OR99-001
OR99-001
OR99-001
OR99-001
OR99-002
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
OR99-005
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
18
-------
CA99-0001
CA99-0002
CA99-0003
CA99-0004
CA99-0005
CA99-0006
CA99-0007
CA99-0008
CA99-0009
CA99-0010
CA99-001 1
CA99-0012
CA99-0013
CA99-001 4
CA99-0015
CA99-001 6
CA99-001 7
CA99-0018
CA99-0019
CA99-0020
CA99-0021
CA99-0022
CA99-0023
CA99-0024
CA99-0025
CA99-0026
CA99-0027
CA99-0028
CA99-0029
CA99-0030
CA99-0031
CA99-0032
CA99-0033
CA99-0034
CA99-0035
CA99-0036
CA99-0037
CA99-0038
CA99-0039
CA99-0040
CA99-0041
CA99-0042
CA99-0043
CA99-0044
CA99-0045
CA99-0046
CA99-0047
CA99-0048
CA99-0049
CA99-0050
CA99-0051
CA99-0052
CA99-0053
CA99-0054
CA99-0055
CA99-0056
CA99-0057
CA99-0058
CA99-0059
CA99-0060
CA99-0061
CA99-0062
CA99-0063
CA99-0064
CA99-0065
CA99-0066
CA99-0067
CA99-0068
CA99-0069
CA99-0070
41.162
40.837
40.824
40.720
40.703
38.287
38.263
38.249
38.104
38.015
38.006
38.006
38.002
36.961
36.859
36.633
36.628
36.537
36.525
35.346
35.318
35.171
35.173
35.161
34.692
34.407
34.354
34.180
34.167
34.097
33.844
33.777
33.742
33.755
33.741
33.730
33.743
33.724
33.719
33.461
33.234
33.145
33.143
32.772
32.755
32.759
32.727
32.726
32.651
32.639
41 .945
41 .947
41 .944
41 .941
41 .937
41 .606
41 .605
41 .547
41 .546
41 .541
41 .028
41 .027
40.644
40.646
40.475
39.427
39.417
39.418
39.361
39.303
-124.118
-124.117
-124.142
-124.238
-124.258
-123.028
-123.012
-122.978
-122.848
-122.917
-122.910
-122.873
-122.865
-122.019
-121.801
-121.845
-121.853
-121.930
-121.936
-120.847
-120.858
-120.737
-120.725
-120.710
-120.597
-119.693
-119.309
-119.230
-119.227
-119.079
-118.395
-118.242
-118.252
-118.154
-118.177
-118.256
-118.140
-118.214
-118.233
-117.702
-117.412
-117.342
-117.339
-117.210
-117.248
-117.219
-117.215
-117.180
-117.129
-117.138
-124.201
-124.204
-124.197
-124.196
-124.196
-124.100
-124.101
-124.081
-124.075
-124.079
-124.112
-124.109
-124.305
-124.304
-124.388
-123.808
-123.812
-123.809
-123.815
-123.794
Big Lagoon
Arcata Bay
Arcata Bay
Humboldt Bay
Humboldt Bay
Bodega Bay
Bodega Bay
Bodega Bay
Tomales Bay
Drakes Bay
Drakes Bay
Drakes Bay
Drakes Bay
Santa Cruz Harbor
Pajaro River
Monterey Harbor
Monterey Harbor
Carmel Bay
Carmel Bay
Morro Bay
Morro Bay
San Luis Obispo Bay
San Luis Obispo Bay
San Luis Obispo Bay
Santa Ynez River
Santa Barbara Harbor
Ventura River
Channel Islands Harbor
Channel Islands Harbor
Point Mugu Lagoon
King Harbor
Los Angeles River
Los Angeles Harbor
Long Beach Harbor
Long Beach Harbor
Los Angeles Harbor
Long Beach Harbor
Los Angeles Harbor
Los Angeles Harbor
Dana Point Harbor
Santa Margarita River
Agua Hedionda Creek
Agua Hedionda Creek
Mission Bay
San Diego River
San Diego River
San Diego Bay
San Diego Bay
San Diego Bay
San Diego Bay
Smith River (CA)
Smith River (CA)
Smith River (CA)
Smith River (CA)
Smith River (CA)
Wilson Creek
Wilson Creek
Klamath River
Klamath River
Klamath River
Little River
Little River
Eel River
Eel River
Bear River
Noyo River
Hare Creek
Hare Creek
Caspar Creek
Big River
7.79
12.5
12.5
12.5
12.5
12.5
12.5
12.5
12.5
12.5
12.5
12.5
12.5
7.79
0.86
7.79
7.79
7.79
7.79
7.79
7.79
7.79
7.79
7.79
0.86
0.86
0.86
0.86
0.86
0.86
0.86
0.86
12.5
7.79
7.79
12.5
7.79
12.5
12.5
0.86
0.86
0.86
0.86
7.79
0.86
0.86
12.5
12.5
12.5
12.5
0.10
0.106
0.106
0.106
0.106
0.08
0.08
0.0346
0.0346
0.0346
0.08
0.08
0.0914
0.0914
0.08
0.0585
0.08
0.08
0.08
0.0585
102.651
268.504
268.504
268.504
268.504
268.504
268.504
268.504
268.504
268.504
268.504
268.504
268.504
102.651
13.837
102.651
102.651
102.651
102.651
102.651
102.651
102.651
102.651
102.651
13.837
13.837
13.837
13.837
13.837
13.837
13.837
13.837
268.504
102.651
102.651
268.504
102.651
268.504
268.504
13.837
13.837
13.837
13.837
102.651
13.837
13.837
268.504
268.504
268.504
268.504
0.654
0.654
0.654
0.654
0.654
0.014
0.014
0.309
0.309
0.309
0.018
0.018
0.219
0.219
0.018
0.427
0.018
0.018
0.014
0.427
CA99-002
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-002
CA99-003
CA99-002
CA99-002
CA99-002
CA99-002
CA99-002
CA99-002
CA99-002
CA99-002
CA99-002
CA99-003
CA99-003
CA99-003
CA99-003
CA99-003
CA99-003
CA99-003
CA99-003
CA99-001
CA99-002
CA99-002
CA99-001
CA99-002
CA99-001
CA99-001
CA99-003
CA99-003
CA99-003
CA99-003
CA99-002
CA99-003
CA99-003
CA99-001
CA99-001
CA99-001
CA99-001
CA99-006
CA99-006
CA99-006
CA99-006
CA99-006
CA99-004
CA99-004
CA99-009
CA99-009
CA99-009
CA99-005
CA99-005
CA99-01 0
CA99-01 0
CA99-005
CA99-007
CA99-005
CA99-005
CA99-004
CA99-007
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N
N
N
N
N
N
N
Y
Y
Y
N
N
Y
Y
N
Y
N
N
N
Y
19
Table continued on next page
-------
CA99-0071 39.226 -123.770 Albion River 0.0914 0.219 CA99-010 Y
CA99-0072 39.225 -123.768 Albion River 0.0914 0.219 CA99-010 Y
CA99-0073 39.227 -123.764 Albion River 0.0914 0.219 CA99-010 Y
CA99-0074 39.103 -123.707 Elk Creek 0.08 0.014 CA99-004 N
CA99-0075 39.102 -123.705 Elk Creek 0.08 0.014 CA99-004 N
CA99-0076 38.954 -123.730 Garcia River 0.0585 0.427 CA99-007 Y
CA99-0077 38.451 -123.127 Russian River 0.0498 0.104 CA99-008 Y
CA99-0078 38.449 -123.125 Russian River 0.0498 0.104 CA99-008 Y
CA99-0079 38.307 -122.995 Estero Americano 0.0585 0.427 CA99-007 Y
CA99-0080 38.270 -122.976 Estero San Antonio 0.0585 0.427 CA99-007 Y
20
-------
2.2 Data Analysis
Analysis of indicator data was conducted by calculation of cumulative distribution
functions (CDFs), an analysis approach that has been used extensively in other EMAP
coastal studies (Summers et al., 1993; Strobel et al.,1994; Hyland et al., 1996). The
CDFs describe the full distribution of indicator values in relation to their areal extent
across the sampling region of interest. The approximate 95% confidence intervals for
the CDFs also were computed based on estimates of variance. A detailed discussion of
methods for calculation of the CDFs used in EMAP analyses is provided in Diaz-Ramos
etal. (1996).
The Horvitz-Thompson ratio estimate of the CDF is given by the formula:
F(x»)=
F(xk) = estimated CDF (proportion) for indicator value x*
n = number of samples
y/= the sample response for site i
x* = the k th CDF response indicator
[0, otherwise
m = selection probability for site i
A
N = the estimated population size
The selection probability for a site is 1/area of the hexagon, e.g. the hexagon area of
California estuaries in the base study in the size class 5-25 km2. When calculating the
mean for a variable, the same equation is used with Y, replacing the indicator function.
21
-------
The Horvitz-Thompson unbiased estimate of the variance for the ratio estimate is given
by the formula:
ZC7:
^2-
v [F(Xk)] = ±L^_
A/2
N = ^]—, cf, = /(y < x*) - F(xk), dj = /(y < x*) - F(x*)
A
F(x*) = estimated CDF (proportion) for indicator value x*
[0, otherwise
xk = the kth indicator level of interest
y, = value of indicator for the ith unit sampled
n-t = inclusion density evaluated at the location
of the ith sample point
ay = joint inclusion density evaluated at the locations
of the ith and jthsample points
n = number of units sampled
The joint inclusion probabilities are given by
71 'a =
1
n
22
-------
When estimating the CDF across several strata, the above estimates for each stratum
must be combined. The equations are
F(xk) = estimated CDF
A
F,(Xk) = estimated CDF for stratum i
Aj = area for stratum i
S = number of strata
A = total area of all strata
and the variance estimate across strata is
v = v
V = estimated variance for all strata
A
Vj = estimated variance for stratum i
AI = area for stratum i
S = number of strata
A = total area of all strata
23
-------
2.3 Indicators
The condition of West Coast estuarine resources was evaluated by collecting data for a
standard set of environmental parameters at all stations within the survey (Table 2-2).
Field procedures followed methods outlined in the USEPA National Coastal Assessment
Field Operations Manual (USEPA, 2001 b). The environmental indicators were similar to
those used in previous EMAP estuarine surveys in other regions of the country
(Weisberg et al., 1992; Macauley et al., 1994, 1995; Strobel et al., 1994, 1995; Hyland
et al., 1996, 1998). Indicators were divided into those representing general habitat
condition (Habitat Indicators), condition of benthic and demersal faunal resources (Biotic
Condition Indicators), and exposure to pollutants (Exposure Indicators). Habitat
indicators describe the general physical and chemical conditions at the study site, and
are often important in providing information used to interpret the results of biotic
condition indicators (e.g., salinity and sediment grain size with regard to benthic
community composition). Biotic condition indicators are measures of the status of the
benthic biological resources in response to site environmental conditions. The
Exposure indicators used in this survey quantify the amounts and types of pollutant
materials (metals, hydrocarbons, pesticides) that may be harmful to the biological
resources present. Some indicators may overlap the above categories. For example,
dissolved oxygen is clearly an indicator of habitat condition, but may also be considered
an exposure indicator because of the potentially harmful effects of low dissolved oxygen
levels to many members of the benthic community.
In addition to the core set of indicators, a number of supplemental indicators were
conducted either by EMAP or by external collaborators during the EMAP Western
Coastal survey (Table 2-3). An additional sediment toxicity test was conducted for the
California stations composing the base study. The amphipod Eohaustorius estuarius
acute toxicity test was used in order to compare the sensitivity of this species with
Ampelisca abdita, which is the most commonly used amphipod bioassay species in the
EMAP program. Scientists with the USGS/BEST program conducted two sediment
porewater toxicity tests using the sea urchin Arbacia punctulata (fertilization toxicity test,
embryo development toxicity test) (USGS, 2000), and conducted the H4IIE bioassay
(bioassay-derived 2,3,7,8-tetrachlorodibenzo - p -dioxin equivalents (TCDD-EQ)) for
exposure offish to planar halogenated hydrocarbons (USGS, 2001). Results of the sea
urchin bioassay tests are included in the present report, while the details of the H4lle
bioassay are provided in USGS (2001). Results of the Eohaustorius toxicity test are not
presented here, since this test was done only with California sediments, but will be
provided in a separate statistical data report for the state of California.
24
-------
Table 2-2. Core environmental indicators for the EMAP Western Coastal survey.
Habitat Indicators
Salinity
Water depth
pH
Water temperature
Total suspended solids
Chlorophyll a concentration
Nutrient concentrations (nitrates,
nitrites, ammonia, & phosphate)
Percent light transmission
Secchi depth
Percent silt-clay of sediments
Percent total organic carbon (TOC)
in sediments
Benthic Condition Indicators
Infaunal species composition
Infaunal abundance
Infaunal species richness and diversity
Demersal fish species composition
Demersal fish abundance
Demersal fish species richness and
diversity
External pathological anomalies in fish
Exposure Indicators
Dissolved oxygen (DO) concentration
Sediment contaminants
Fish tissue contaminants
Sediment toxicity (Ampelisca abdita
acute toxicity test)
25
-------
Table 2-3. Environmental indicators under development or conducted by collaborators
during the EMAP Western Coastal survey.
Benthic Condition Indicators
West Coast benthic infaunal index - EMAP
Exposure Indicators
Sediment toxicity (amphipod Eohaustorius estuarius acute toxicity test) - EMAP
(California only)
Sediment porewater toxicity (sea urchin Arbacia punctulata fertilization toxicity test)
USGS/BEST1
Sediment porewater toxicity (sea urchin Arbacia punctulata embryo development
toxicity test) - USGS/BEST1
H4IIE Bioassay-derived 2,3,7,8-tetrachlorodibenzo - p -dioxin equivalents (TCDD-EQ)
for exposure offish to planar halogenated hydrocarbons - USGS/BEST2
1 USGS, 2000
2 USGS, 2001
26
-------
2.3.1 Water Measurements
2.3.1.1 Hydrographic Profile
Water column profiles were performed at each site to measure dissolved oxygen (DO),
salinity, temperature, pH, and depth. Both secchi depth and a measurement of light
attenuation using photosynthetically active radiation (PAR) were made at each station.
Methods and procedures used for hydrographic profiling follow guidance provided in the
NCA Quality Assurance Project Plan document (US EPA, 2001).
Basic water quality parameters were measured by different instruments in each state.
Washington field crews used the Seabird SBE 19 CTD with data logging capability. In
Oregon there were two field crews. The Oregon Dept. of Environmental Quality field
crew used a YSI 6920 datasonde. The field crew provided by National Marine Fisheries
Service used a Hydrolab datasonde. California used a Hydrolab Datasonde 4a with a
cable connection to a deck display. Prior to conducting a CTD (Conductivity,
Temperature, Depth) cast, the instrument was allowed 2-3 minutes of warmup while
being maintained near the surface, after which the instrument was slowly lowered at the
rate of approximately 1 meter per second during the down cast. Individual
measurements were made at discrete intervals (with sufficient time for equilibration) as
follows:
Shallow sites (< 2 m) - 0.5-m intervals;
Typical depths (>2<10 m) - 0.5 m (near-surface) and every 1-m interval to near-
bottom (0.5 m off-bottom);
Deep sites (>10 m) - 0.5 m (near-surface) and every 1-m interval to 10 m, then at
5-m intervals, thereafter, to near-bottom (0.5 m off-bottom).
Near-bottom conditions were measured at 0.5 m above the bottom by first ascertaining
whether the instrument was on the bottom (slack line/cable), and then pulling it up
approximately 0.5 m. A delay of 2-3 minutes was used to allow disturbed conditions to
settle before taking the near-bottom measurements. The profile was repeated on the
ascent and recorded for validation purposes, but only data from the descent were
reported in the final data.
Measurements of light penetration were recorded using a hand-held LiCor LI-1400 light
meter for conditions at discrete depth intervals in a manner similar to that for profiling
water quality parameters with the hand-held water quality probes. The underwater
sensor was hand lowered according to the regime described above and at each discrete
interval, the deck reading and underwater reading were recorded. If the light
measurements became negative before reaching bottom, the measurement was
terminated at that depth. The profile was repeated on the ascent. As an indicator of
water column light conditions, the transmissivity at 1 m depth was calculated.
27
-------
The California field crew measured ambient light data in two ways. The Hydrolab
datasonde unit had a LiCor spherical irradiance sensor (LI -193SA) mounted to the
sensor package. For boat deployments, the deck sensor recording ambient light was a
cosine collector (LI-190SA)). However, many of the California sample locations were
too shallow to allow sampling from a boat, and required walking in to the sample site. At
these stations, the field crew took ambient irradiance with the spherical sensor in air,
and then took several subsurface readings with the same sensor. The difference in
geometry between the deck reference sensor and submerged sensor was corrected for
during the analysis of light transmission. An empirical comparison of similar LiCor
spherical and flat sensors, both calibrated for air measurements, was conducted. The
spherical sensor collected an average of two times the light measured by the flat
sensor. All ambient light measurements for California stations sampled by boat were
first corrected by this factor. The minimum depth where the first submerged light
reading was taken varied widely among stations, which made inter-station comparison
difficult. Therefore, the submerged and corresponding in air light measurements,
together with the depth of the measurement, were used to compute the light extinction
coefficient k, using the relationship k = (In(l0) - ln(ld))/d , where I0 = in air measure of
light, ld = submerged light, and d = the depth of the first submerged light measurement.
The value of k that was computed was assumed to characterize the light attenuation
down to a depth of 1 m, and light at a depth of 1 m (I1m) was then calculated as I1m = e("
kd), where d = 1m. Percent light transmission at 1m was then computed as (I1m/10) * 100.
Secchi depth was determined by using a standard 20-cm diameter black and white
secchi disc. The disc was lowered to the depth at which it could no longer be discerned,
then was slowly retrieved until it just reappeared. The depth of reappearance was
recorded as secchi depth (rounded to the nearest 0.5 m).
2.3.1.2 Water Quality Indicators
The water column was sampled at each site for dissolved nutrients (N and P species),
chlorophyll a concentration, and total suspended solids (TSS). Sampling varied slightly
among the states but generally followed the guidance provided in the NCA Quality
Assurance Project Plan document (US EPA, 2001). At shallow sites (<2 m), water
samples were taken at 0.5 m (near-surface) and 0.5 m off-bottom. If the depth was so
shallow that the near-surface and near-bottom overlapped, then only a mid-depth
sample was taken. For sites deeper than 2 m, samples were taken at 0.5 m (near-
surface), mid-depth, and 0.5 m off-bottom.
For TSS analysis, 1 liter of unfiltered seawater was collected at the depths described
above. The samples were held in 1-L polypropylene bottles on wet ice in the field and
stored at 4°C until analyzed.
For Washington samples, water used for nutrient, chlorophyll, and dissolved oxygen
samples was collected from discrete depths using 1.7-liter Nisken bottle and transferred
to two 66-ml plastic bottles. The chlorophyll samples were filtered by placing them in a
28
-------
funnel containing a 0.7-um GFF filter attached to a receiving bottle. A hand pump was
used to pull the seawater past the filter and into a receiving flask. The GFF filter was
then folded in half and placed in a labeled glass centrifuge tube containing 10 ml of 90
% acetone, and placed on ice until the tubes could be frozen at the end of the day. A
0.45-um syringe filter was used with a pre-cleaned, 60-ml plastic syringe to filter
approximately 40 ml of water for nutrient analyses into 60-ml plastic bottles.
In California, samples were obtained by using a Wildco 1.2-liter stainless steel
Kemmerer sampler. A second water sample was collected from each of the same
depths and an approximately 1-liter subsample was poured into a clean, wide-mouth
polycarbonate container for the chlorophyll and nutrient analyses. Two disposable,
graduated 50-cc polypropylene syringes fitted with a stainless steel or polypropylene
filtering assembly were used to filter the water sample through 0.7-um GFF filters, and
the volume of water (up to 200 ml for each syringe) filtered was recorded. Both filters
were carefully removed using tweezers, folded once upon the pigment side, placed in a
prelabeled, disposable petri dish, and capped. The petri dish was wrapped in aluminum
foil, placed in a small styrofoam ice chest with several pounds of dry ice, and kept
frozen until analyzed. The syringe and filtering assembly were washed with deionized
water and stored in a clean compartment between sampling stations. For nutrients,
approximately 40 ml of filtrate from the chlorophyll filtration (surface water) were
collected into two prelabeled, clean 60-ml Nalgene screw-capped bottles, stored in the
dry ice chest, and kept frozen on dry ice until analyzed.
Dissolved Oxygen was measured at Washington stations with a Beckman DO sensor
deployed on the Seabird CTD, at Oregon stations with a Yellow Springs Instruments
model 6562 DO sensor on the YSI datasonde, and at California stations with a Hydrolab
DO sensor on the Hydrolab datasonde.
2.3.2 Sediment Toxicity Testing
2.3.2.1 Sediment Collection for Toxicity Testing, Chemical Analysis and Grain Size
Combined sediment for toxicity testing and chemical analysis was collected at all sites
from the top 2-3 centimeters of surficial sediment. Procedures for sediment collection
followed the guidance provided in the NCA Quality Assurance Project Plan document
(US EPA, 2001). Where possible, sediment grabs were taken with a 0.1 -m2 van Veen
sampler. The top 2-3 centimeters of surficial sediment were scooped from each
individual grab, composited in a pre-cleaned container and homogenized within the
container by thorough stirring. Sediment from 2-9 grabs was composited to collect
approximately 6 liters of sediment. Where station depth precluded sampling with a boat
and van Veen grab, the sampling crew walked in to the sample site, and the top 2-3 cm
of sediment at the site was scooped from the sediment surface and processed similarly
to sediment collected by grab. This occurred at the following stations: 4 sites in
Washington: WA99-0015, WA99-0016, WA99-0017, WA99-0019; 33 sites in California:
29
-------
CA99-0001, CA99-0015, CA99-0021, CA99-0025, CA99-0030, CA99-0037, CA99-0041,
CA99-0045-46, CA99-0051-57, CA99-0059-65, CA99-0067-71, CA99-0073-74, CA99-
0076, CA99-0079-80. The composited sediment was held on ice and distributed to
individual containers for toxicity testing and chemical analyses either on board the
research vessel or at the laboratory. Aliquots of the homogenized sediment were
distributed to pre-cleaned containers for analysis of sediment organics, trace metals,
grain size and toxicity testing. Toxicity-test sediment was held at 4°C to await initiation of
toxicity testing within 7 days of collection.
2.3.2.2 Laboratory Test Methods
2.3.2.2.1 Amphipod Toxicity Tests
The 10-day, solid-phase toxicity test with the marine amphipod Ampelisca abdita was
used to evaluate potential toxicity of sediments from all sites. Procedures followed the
general guidelines provided in ASTM Protocol E1367-92 (ASTM, 1991), the EPA
amphipod sediment toxicity test manual (USEPA,1994a) and the EMAP Laboratory
Methods Manual (USEPA,1994b). The Ampelisca test is a 10-d acute toxicity test which
measures the effect of sediment exposure on amphipod survival under static aerated
conditions.
Approximately 3-3.5 L of surface sediments (composite of upper 2-3 cm from multiple
grabs) were collected from the sampling sites and stored in glass or polyethylene jars at
4 °C in the dark until testing. Toxicity tests were conducted with subsamples of the same
sediment on which the analysis of organic and trace metal contaminants and other
sediment characteristics was performed.
Ampelisca abdita were collected from the Narrow (=Pettaquamscutt) River, Rhode
Island, by Eastern Aquatic Biosupply, or from San Pablo Bay in the San Francisco
Estuary by Brezina and Associates. Amphipods were shipped via overnight carrier to the
Marine Pollution Studies Laboratory at Granite Canyon, CA (CA and WA sediments),
Southern California Coastal Water Research Project (SCCWRP - CA sediments) or the
Northwestern Aquatic Sciences, Inc., laboratory in Newport, Oregon (OR sediments),
where the Ampelisca tests were conducted. Amphipods were acclimated for 2-9 days
prior to testing. During the acclimation period, the amphipods were not fed (WA and CA)
or were fed a commercially available dried algal mix (OR). Healthy juvenile amphipods of
approximately the same size (0.5-1.0 mm) were used to initiate tests. The general health
of each batch of amphipods was evaluated in a reference toxicity test (i.e., "positive
control"), which was run for 96 h in a dilution series with seawater (no sediment phase)
and the reference toxicants cadmium chloride or sodium dodecyl sulfate (SDS). LC50
values for reference toxicants were computed for comparison with other reported toxicity
ranges for the same reference toxicant and test species.
30
-------
Treatments for the definitive tests with field samples consisted of five replicates of each
field sediment sample (100% sediment) and a negative control. A negative control was
run with each batch of field samples, which ranged from 4 to18 samples per batch.
Control sediment was ambient sediment from the amphipod collection sites. Twenty
amphipods were randomly distributed to each of five replicates per each treatment
including the control. Amphipods were not fed during the tests. All tests were
conducted under static conditions with aeration, and were monitored for water quality
(temperature, salinity, dissolved oxygen, pH, and total ammonia in the overlying water).
Target test temperature for A. abdita was 20 °C and target salinity was 28 psu.
The negative controls provided a basis of comparison for determining statistical
differences in survival in the field sediments. In addition, control survival provided a
measure of the acceptability of final test results. Test results with A. abdita were
considered valid if mean control survival (among the 5 replicates) was not less than
90% and survival in no single control replicate was less than 80%. Test batches where
these QA requirements were not met were not included in the CDF analysis.
One-liter glass containers with covers were used as test chambers. Each chamber was
filled with 200 ml of sediment and 600-800 ml of filtered seawater. The sediment was
press-sieved, through either a 1.0-mm screen for control samples or a 2.0-mm screen
for field samples, to remove ambient fauna prior to placing the sediment in a test
chamber. Light was held constant during the 10-day test to inhibit amphipod emergence
from the sediment, thus maximizing exposure to the test sediment.
At the conclusion of a test, the sediment from each chamber was sieved through a 0.5-
mm screen to remove amphipods. The number of animals dead, alive, or missing was
recorded. Sediments with >10% missing animals were re-examined under a dissecting
microscope to ensure that no living specimens had been missed. Amphipods still
unaccounted for were considered to have died and decomposed in the sediment.
A variety of quality control procedures were incorporated to assure acceptability of
amphipod test results and comparability of the data with other studies. As described
above, these provisions included the use of standard ASTM and EMAP protocols,
positive controls run with a reference toxicant, negative "performance" controls run with
reference sediment from the amphipod collection site, and routine monitoring of water
quality variables to identify any departures from optimum tolerance ranges.
2.3.2.2.2 Sea Urchin Toxicity Tests
The Biomonitoring and Environmental Status and Trends Program (BEST) of the U.S.
Geological Survey obtained sediment samples collected by EMAP and conducted two
types of sea urchin toxicity tests. The fertilization and embryological development toxicity
tests were conducted with sediment porewater using gametes of the sea urchin Arbacia
punctulata. Methods and results are described in a technical report (USGS, 2000).
31
-------
Sediments for testing were held on ice or refrigerated at 4°C and shipped in insulated
coolers within 7 days to the BEST laboratory. Pore water was extracted from the test
sediments within 24 hours of receipt using a pneumatic device, centrifuged to remove
suspended particulate material, then stored frozen. Sediments that were received by the
BEST laboratory at temperatures exceeding acceptable temperature criteria were
excluded from the CDF analysis.
Sediment pore water was thawed two days prior to testing and stored at 4°C. Water
quality parameters (salinity, temperature, DO) were measured in the thawed pore water
and adjusted if necessary. Samples were tested at a temperature and salinity of 20 +
2°C and 30 + 1 psu. Other water quality parameters that were measured included
dissolved oxygen, pH, sulfide, ammonia and dissolved organic carbon.
Toxicity was determined using percent fertilization and embryological development
(percent normal pluteus stage) as endpoints with gametes of the sea urchin Arbacia
punctulata. A seawater dilution series (100, 50 and 25%) was used to determine the
toxicity of the sediment porewater samples. Filtered seawater and reconstituted brine
were used as dilution blanks. Reference pore water from an uncontaminated site in
Redfish Bay, TX, was included in each test as a negative control. A dilution series with
sodium dodecyl sulfate was used as a positive control. Toxicity was determined with
statistical comparisons among treatments using ANOVA and Dunnett's one-tailed t-test
on the arcsine square root transformed data.
2.3.3 Biotic Condition Indicators
2.3.3.1 Benthic Community Structure
Sediment samples to enumerate the benthic infauna were collected at all sampling sites
unless rocky bottom or other factors prohibited obtaining a benthic sample (see section
2.6). Procedures followed the guidance provided in the NCA Quality Assurance Project
Plan document (US EPA, 2001). The standard sampling gear for all three states was a
0.1 -m2 van Veen grab sampler. All Oregon sites were sampled using this gear. In both
Washington and California, some stations in shallow water required modified methods
when field crews walked into the site. In California, sites with a water depth less than
approximately 1 meter were sampled with hand-held cores. At these shallower areas, a
composite of sixteen 0.0065-m2 cores was taken, for a total surface area of 0.1-m2.
Eight of the base California stations and 23 of the Northern California intensive sites
were sampled with these cores. To evaluate the efficiency of smaller sample sizes, a
single 0.0065-m2 core was taken from the van Veen grabs at 24 sites in Southern
California. For this analysis, the results from the sub-cores and the remainder of the
van Veen grab were combined. In Washington, four shallow-water sites (WA99-0015,
WA99-0016, WA99-0017, WA99-0019) were sampled using a 5-gallon bucket sampler
with an area of 0.049 m2. Because of the difference in area, these four samples were
excluded from the analysis of benthic community structure.
32
-------
The majority of the grab and core samples penetrated a minimum of 5 cm deep. The
eleven samples that penetrated 3-4 cm are included in the present analysis. After
collection, samples were sieved through nested 0.5-mm and 1.0-mm mesh screens. An
elutriation process was used to minimize damage to soft-bodied animals and the
material retained on the screens was relaxed in 1 kg of MgS04 per 20 L of seawater for
30 minutes. The residue was then preserved in the field in sodium borate-buffered 10%
formalin.
The preserved samples were sent to analytical laboratories where they were transferred
to 70% ethanol within 2 weeks of field collection. The 1.0-mm mesh screen samples
were then sorted from the debris. The 0.5-mm mesh samples were not included as part
of EMAP West and were not sorted. The organisms were then identified to the lowest
practical taxonomic level (most often species), and counted by the primary taxonomists
(see Table 2-10). Secondary QA taxonomists ensured that uniform nomenclature was
used across the entire Western Coastal EMAP region; these recognized taxonomic
experts identified and resolved taxonomic discrepancies among the sets of primary
taxonomists. In the analyses for this report, all insect taxa were grouped as Insecta.
Individual insect taxa will be identified in later versions of the database.
The benthic infaunal data were used to compute total numbers of individuals and total
number of species per 0.1 -m2 sample. The Shannon-Weaver information diversity
index H' was calculated (log base 2) per 0.1-m2 sample. Species were classified as
native, nonindigenous, cryptogenic, or indeterminate. Cryptogenic species are species
of uncertain geographic origin (Carlton, 1996), while indeterminate taxa are those taxa
not identified to a sufficiently low level to classify as native, nonindigenous, or
cryptogenic (Lee et al., in press). Species were classified using Cohen and Carlton
(1995) as the primary source and a report by TN and Associates (2001) for taxa not
classified by Cohen and Carlton. The TN and A report specifically classified the benthic
species collected by the 1999 EMAP survey as native, nonindigenous, or cryptogenic.
2.3.3.2 Fish Trawls
Fish trawls were conducted at each site, where possible, to collect fish/shellfish for
community structure and abundance estimates, collect target species for contaminant
analyses, and collect specimens for histopathological examination. In some cases, it
was necessary to use beach seines instead of trawls to collect fish for tissue analysis.
Only trawls were used to evaluate fish community structure because consistency
between beach seines was impossible to maintain.
Trawls were conducted by using a 16-ft otter trawl with 1.5-inch mesh in the body and
wings and 1.25-inch mesh in the cod end. Community structure data (i.e, the fish data
on richness and abundance and individual lengths) were based on a trawl(s) of 10
minute duration. In open water, the trawl was conducted in a straight line with the site
location near center. Timing of the trawl began after the length of towline had been
payed out and the net began its plow. The speed over bottom was approximately 2
33
-------
knots. When possible, trawling was conducted for the entire 10-minute period, after
which the ship's transmission was placed in neutral and the trawl net retrieved and
brought aboard. In constrained areas where 10-minute trawls were not possible, two 5-
minute trawls were conducted. Contents of the bag were emptied into an appropriately
sized trough or livebox to await sorting, identifying, measuring, and sub-sampling.
Trawling was the last field activity performed because of possible disturbance to
conditions at the site. Every effort was made to return any rare or endangered species
back to the water before they suffered undue stress.
In Oregon and Washington, fish for tissue and histopathological analysis were collected
with a 120-foot long beach seine where waters were too shallow to use the otter trawl.
The seine had 1-inch mesh in the wings and 3/8-inch mesh in the bag end. In
California, a 100-foot seine with 1/8-inch mesh was used for fish collections in shallow
waters.
2.3.3.3 Fish Community Structure
Fish from a successful trawl (full time on bottom with no hangs or other interruptions)
were first sorted by species and identified to genus and species. Up to thirty individuals
per species were measured by using a fish measuring board to the nearest centimeter
(fork length when tail forked, otherwise overall length - snout to tip of caudal). The
lengths were recorded on a field form and a total count made for each species. All fish
not retained for histopathology or tissue chemistry were returned to the estuary.
2.3.3.4 Fish Contaminant Sampling
Several species of demersal soles, flounders, and dabs were designated as target
species for the analyses of chemical contaminants in whole-body tissue. These flatfish
are common along the entire U.S. Pacific Coast and are intimately associated with the
sediments. Where the target flatfish species were not collected in sufficient numbers,
perchiform species were collected. These species live in the water column but feed
primarily or opportunistically on the benthos. In cases where neither flatfish species nor
perches were collected, other species that feed primarily or opportunistically on the
benthos were collected for tissue analysis. A total of 16 species were collected for
tissue analysis in the base study sites in all three states and a total of 17 species if the
intensive study stations are included. The species analyzed for tissue contaminants
were (species occurring in no or only one base study station are identified):
Pleuronectiformes
Citharichthys sordidus - Pacific sanddab
Citharichthys stigmaeus - speckled sanddab
Paralichthys californicus - California halibut
Platichthys stellatus - starry flounder
Pleuronectes isolepis - butter sole (1 base study station OR)
34
-------
Pleuronectes vetulus - English sole
Psettichthys melanostictus - sand sole
Symphurus atricauda - California tonguefish (1 base study station CA)
Perciformes
Cymatogaster aggregata - shiner perch
Embiotoca lateralis - stripped sea perch (1 base study station OR)
Gasterosteus aculeatus - threespine stickleback (1 base study and
1 intensive study station CA)
Genyonemus lineatus - white croaker
Paralabrax maculatofasciatus - spotted sand bass (1 base study station CA)
Paralabrax nebulifer - barred sand bass
Other
Atherinops affinis - topsmelt (1 base station CA)
Leptocottus armatus - Pacific staghorn sculpin
Oligocottus rimensis - saddleback sculpin (2 Northern CA intensive study
stations)
At sites where target species were captured in sufficient numbers, 3 to 30 individuals of
a species were combined into a composited sample. Due to their small size, up to 220
individual Gasterosteus aculeatus (threespine stickleback) were composited to obtain a
sufficient tissue sample at one of the intensive sites in California. In all cases, the fish
were first measured and recorded on the sampling form as chemistry fish. The fish were
then rinsed with site water, individually wrapped with heavy duty aluminum foil (with the
length of each individual fish printed on the foil wrap to facilitate the possible later
selection of specific individuals at the laboratory), and placed together in a plastic,
Ziploc bag labeled with the Station ID Code and a Species ID Code (e.g., the first four
letters of both the genus and species). The fish tissue chemistry samples were held on
wet ice in the field until they were transferred to shore and frozen to await laboratory
analysis.
2.3.3.5 Fish Contaminant Chemistry Analyses
Neutral organic and metal contaminants were measured in the whole-body tissues of
the seventeen species of fish listed above (Section 2.4.3.4). Contaminant
concentrations were determined for each of the composited tissue samples. A total of
11 metals, 20 polychlorinated biphenyls (PCBs), DDT and its primary metabolites, and
an additional 13 pesticides were measured in the fish samples. Oregon measured PCB
110 and PCB77 as PCB 110/77. Compounds not measured in all three states (e.g.,
PCB187) are not reported here. PAHs were not measured in fish tissues because of
their rapid metabolism in vertebrates. The analytes measured in all three states in fish
and sediments are summarized in Table 2-4. Table 2-5 summarizes the sample
collection, preservation, and holding time requirements for sediment and tissue
samples. Table 2-6 summarizes the analytical methods used in the three states for
35
-------
both sediments and tissues. For tissue chemistry analyses, the NCA Quality Assurance
Program Plan (EPA 2001) recommended that internal standards known as surrogates
be run, and suggested that reported concentrations for analytes be adjusted to correct
for recovery of surrogates. The state analytical laboratories generally used surrogates
only as an indication of whether a re-extraction of a sample was required.
2.3.3.6 Fish Gross Pathology
Any fish pathologies (e.g., tumors) observed on fish collected in the trawls were
photographed, then excised and placed into labeled pathology containers, and put
immediately into Dietrich's solution. Excised tissue included the entire pathology and
some adjacent healthy tissue. Pathology information, including cartridge number, fish
species, size, station ID, trawl number, pathology location, description, and sample
depth was recorded onto a Cumulative Fish Pathology Log. At the end of the field
collection, all samples were sent to Dr. Mark Meyers at NMFS/NOAA in Seattle for
analysis. A separate fish pathology report will be prepared by NOAA.
2.3.4 Sediment Chemistry
A total of 15 metals, 20 PCB congeners (PCBs), DDT and its primary metabolites, 12
pesticides, 21 polynuclear aromatic aromatics (PAHs), and total organic carbon (TOC)
were measured in sediments in all three states (Table 2-4). Oregon measured PCB 110
and PCB77 as PCB 110/77. Compounds not measured in all three states (e.g.,
hexaclorobenzene) are not reported here. With a few additions, this suite of
compounds is the same as measured in the NOAA NS&T Program.
Sediment for chemical analysis was collected from the top 2-3 centimeters in benthic
grabs and stored in pre-cleaned glass containers (see Table 2-5). Sediment samples
for chemical analysis were taken from the same sediment composite used for the
sediment toxicity tests. Approximately 250-300 ml of sediment was collected from each
station for analysis of the organic pollutants and another 250-300 ml for analysis of the
metals and TOC (Table 2-5). Table 2-6 lists the analytical methods used for each
compound. For sediment chemistry analyses, the NCA Quality Assurance Program
Plan (EPA 2001) recommended that internal standards known as surrogates be run,
and suggested that reported concentrations for analytes be adjusted to correct for
recovery of surrogates. The state analytical laboratories generally used surrogates only
as an indication of whether re-extraction of a sample was required. The exception was
the laboratory for the State of Washington which made surrogate recovery corrections
to the reported values for PAHs only.
36
-------
Table 2-4. Compounds analyzed in all three states in sediments and fish tissues. PAHs and TOC were analyzed only in
sediments. Toxaphene was analyzed only in tissues. Oregon combined the analysis of PCB110 and PCB77 into a single
measurement of PCB 110/77.
Polyaromatic Hydrocarbons
(PAHs)
Low Molecular Weight PAHs (sediments only)
1 -methy Inaphthalene
1 -methy Iphenanthrene
2-methy Inaphthalene
2,6-dimethylnaphthalene
2 , 3 , 5 - trimethy Inaphthalene
Acenaphthene
Acenaphthylene
Anthracene
Biphenyl
Fluorene
Naphthalene
High Molecular Weight PAHs (sediments only)
Benz(a)anthracene
Benzo(a)pyrene
Benzo(b)fluoranthene
Benzo(k)fluoranthene
Benzo(g,h,i)perylene
Chrysene
Dibenz(a,h)anthracene
Fluoranthene
Indeno( 1 ,2,3-c,d)pyrene
Pyrene
PCB Congeners
(Congener Number and
Compound)
8: 2,4'-dichlorobiphenyl
18: 2,2',5-trichlorobiphenyl
28: 2,4,4'-trichlorobiphenyl
44: 2,2',3,5'-tetrachlorobiphenyl
52: 2,2',5,5'-tetrachlorobiphenyl
66: 2,3',4,4'-tetrachlorobiphenyl
77: 3,3',4,4'-tetrachlorobiphenyl
101 : 2,2',4,5,5'-pentachlorobiphenyl
105: 2,3,3',4,4'-pentachlorobiphenyl
1 10: 2,3,3',4',6-pentachlorobiphenyl
118: 2,3',4,4',5-pentachlorobiphenyl
126: 3,3',4,4',5-pentachlorobiphenyl
128: 2,2',3,3',454'-hexachlorobiphenyl
1 38: 2,2',3,4,4',5'-hexachlorobiphenyl
153: 2,2',4,4',5,5'-hexachlorobiphenyl
170: 2,2',3,3',4,4',5-heptachlorobiphenyl
1 80: 2,2',3,4,4',5,5'-heptachlorobiphenyl
195: 2,2',3,3',4,4',5,6-octachlorobiphenyl
206: 2,2',3,3',4,4',5,5',6-nonachlorobiphenyl
209: 2,2'3,3',4,4',555',656 '-decachlorobiphenyl
DDT and Other
Chlorinated
Pesticides
DDTs
2,4-DDD
4,4'-DDD
2,4'-DDE
4,4'-DDE
2,4'-DDT
4,4'-DDT
Cyclopentadienes
Aldrin
Dieldrin
Endrin
Chlordanes
Alpha-Chlordane
Trans-Nonachlor
Others
Endosulfan 1
Endosulfan II
Endosulfan Sulfate
Lindane (gamma-BHC)
Mi rex
Toxaphene (tissue only)
Metals and Misc.
Metals
Aluminum
Antimony (sediment only)
Arsenic
Cadmium
Chromium
Copper
Iron (sediment only)
Lead
Manganese (sediment
only)
Mercury
Nickel
Selenium
Silver
Miscellaneous
Total organic carbon
(sediment only)
CO
-------
Table 2-5. Summary of EMAP-Coastal chemistry sample collection, preservation, and holding time requirements for
sediment and fish tissues. Modified from Table 5-3 (U.S. EPA, 2001 a).
Parameter
Sediment -
Organics
Sediment -
Metals
Sediment -
TOO
Fish tissue
Container Volume
500-ml pre- 250 -300 ml
cleaned glass
125-mlHDPE 100 -150 ml
wide-mouth
bottle
Glass jar 100 -150 ml
Whole fish NA
individually
wrapped in Al
foil, then
placed in
water-tight
plastic bag.
Sample Size
300 g
(approx.)
75- 100 g
(approx.)
30 -50 ml
(approx.)
NA
Sample
Preservation
Freeze (-1 8°
C)
Freeze (-1 8°
C)
Cool (4° C)
Freeze (-1 8°
C)
Max. Max. Extract
Sampling Holding Time
Holding Time
1 year 40 days
1 year a
6 months a
1 year 40 days
CO
00
a - No EPA criterion exists. Every effort should be made to analyze the sample as soon as possible following extraction
or, in the case of metals, digestion.
-------
Table 2-6. Methods used to analyze for contaminants in sediments and tissues.
NA = not analyzed.
Analyte
Aluminum
Antimony
Arsenic
Cadmium
Chromium
Copper
Iron
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Tin
Zinc
PCB congeners
DDT, ODD, and
DDE
PAHs
Aldrin
Alpha-Chlordane
Dieldrin
Endosulfan 1
Endosulfan II
CA
Sediment/Tissue
ICPMS/ICPMS
ICPMS/ICPMS
ICPMS/ICPMS
ICPMS/ICPMS
ICPMS/ICPMS
ICPMS/ICPMS
FAA/NA
ICPMS/ICPMS
ICPMS/ICPMS
FIMS/FIMS
ICPMS/ICPMS
HAA/ICPMS
GFAA/ICPMS
ICPMS/NA
ICPMS/ICPMS
GCMS/GCMS
GCMS/GCMS
GCMS/NA
GCMS/GCMS
GCMS/GCMS
GCMS/GCMS
GCMS/GCMS
GCMS/GCMS
OR
Sediment/Tissue
ICPAES/ICPAES
G FAA/NA
ICPAES/ICPAES
GFAA/GFAA
ICPAES/ICPAES
ICPAES/ICPAES
ICPAES/ICPAES
ICPAES/GFAA
ICPAES/NA
CVAA/CVAA
ICPAES/ICPAES
HAA/HAA
GFAA/GFAA
ICPAES/ICPAES
ICPAES/ICPAES
GCECD/GCECD
GCECD/GCECD
GCMS/NA
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
WA
Sediment/Tissue
ICPAES/ICPAES
ICPMS/NA
AA/AA
ICPMS/ICPMS
ICPAES/ICPMS
ICPAES/ICPMS
ICPAES/ICPAES
ICPMS/ICPMS
ICPAES/NA
CVAA/CVAA
ICPAES/ICPMS
AA/AA (FURNACE)
ICPMS/ICPMS
ICPMS/ICPMS
ICPAES/ICPMS
GCECD/GCECD
GCECD/GCECD
GCMS/NA
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
Table continued on next page
39
-------
Endosulfan
Sulfate
Endrin
Heptachlor
Heptachlor
Epoxide
Lindane
(gamma-BHC)
Mi rex
Trans-Nonachlor
TOO
Percent fines
GCMS/GCMS
GCMS/GCMS
GCMS/GCMS
GCMS/GCMS
GCMS/GCMS
GCMS/GCMS
GCMS/GCMS
MARPCN I/NA
wet sieve/NA
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
EPA415.1/NA
gravimetric/NA
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
GCECD/GCECD
PSEP-TOC/NA
PSEP86/NA
Analytical Methods: CVAA = cold vapor atomic absorption, FAA = flame atomic
absorption, FIMS = flow injection mercury system, GCECD = gas chromatography with
electron capture detection, GCMS = gas chromatography/mass spectroscopy, GFAA =
graphite furnace atomic absorption spectrometry, ICPAES = inductively coupled
plasma/atomic emission spectrometry, ICPMS = inductively coupled plasma/mass
spectrometry , HAA = hydride atomic absorption, MARPCN I = high temperature
combustion method.
40
-------
2.4 Quality Assurance/ Quality Control
The quality assurance/quality control (QA/QC) program for the Western Coastal EMAP
program is defined by the "Environmental Monitoring and Assessment Program
(EMAP): National Coastal Assessment Quality Assurance Project Plan 2001-2004" (US
EPA, 2001 a). The NCA has established Data Quality Objectives (DQO) for estimates of
current status for indicators of condition which are stated as: "For each indicator of
condition, estimate the portion of the resource in degraded condition within ±10% for the
overall system and ±10% for subregions (i.e., states) with 90% confidence based on a
completed sampling regime." An assessment of this standard for the combined
1999/2000 data from the states of Washington, Oregon and California is presented in
the Quality Assurance Appendix of the National Coastal Condition Report II (EPA,
2004). The level of uncertainty for the combined west coast data set for all major
indicators was < 5%.
In general, the quality assurance elements for the EMAP Western Coastal program
included initial training workshops on all sampling and analysis requirements and initial
laboratory capability exercises, program-wide audits of field and laboratory operations,
documentation of chain-of-custody, and maintaining open lines of communication and
information exchange. Information management needs were demonstrated to all
participants by the Western Coastal EMAP information manager. Other quality control
measures were incorporated to assure data reliability and comparability and are
described in the NCA plan. These include the use of standard NCA protocols, routine
instrument calibrations, measures of analytical accuracy and precision (e.g., analysis of
standard reference materials, spiked samples, and field and laboratory replicates),
measures of the quality of test organisms and overall data acceptability in sediment
bioassays (e.g., use of positive and negative controls), range checks on the various
types of data, cross-checks between original data sheets (field or lab) and the various
computer-entered data sets, and participation in intercalibration exercises.
Accuracy is used to estimate systematic error (measured vs. true or expected), while
precision is used to determine random error (variability between individual
measurements). Collectively, they provide an estimate of the total error or uncertainty
associated with an individual measured value. Measurement quality objectives (MQO)
for all NCA field and laboratory parameters are expressed in terms of accuracy,
precision, and completeness goals in the NCA QA Project Plan (US EPA, 2001 a, Table
A7-1). These MQOs were established from considerations of instrument manufacturers
specifications, scientific experience, and/or historical data. However, accuracy and
precision goals may not be definable for all parameters due to the nature of the
measurement type (e.g., fish pathology, no expected value).
41
-------
2.4.1 QA of Chemical Analyses
Details of the quality assurance procedures used to generate chemical concentrations
within both sediments and tissue samples with acceptable levels of precision and
accuracy are given in U.S. EPA (2001 a). Briefly, a performance-based approach was
used, which depending upon the compound included 1) continuous laboratory evaluation
through the use of Certified Reference Materials (CRMs) and/or Laboratory Control
Materials (LCMs), 2) laboratory spiked sample matrices, 3) laboratory reagent blanks,
4) calibration standards, and 5) laboratory and field replicates.
Control limit criteria for "relative accuracy" were based on comparing the laboratory's
value to the true or "accepted" values in CRMs or LCMs (see U.S. EPA, 2001 a for
details). The specific requirements for PAHs and PCBs/pesticides are that the "Lab's
value should be within ±30% of true value on average for all analytes; not to exceed
±35% of true value for more than 30% of individual analytes." (U.S. EPA 2001 a). In
addition to evaluating the individual PAH and PCB analytes, relative accuracy for total
PAHs and PCBs was determined for each combined group of organic compounds. Metals
and other inorganic compounds were treated individually, and the laboratory's value for
each analyte should be within ±20% of the upper or lower 95% confidence limit of the
CRM or LCM. Because of inherent variability at low concentrations, these control limit
criteria were applied only to analytes having CRM or LCM values >10 times the MDL.
To evaluate precision, each laboratory periodically analyzed CRM or LCM samples using
a control limit of 3 standard deviations of the mean (Taylor, 1987). Based on analysis of
all the samples in a given year, an overall relative standard deviation (RSD, or coefficient
of variation) of less than 30% was considered acceptable precision for analytes with
CRM concentrations > 10 times the MDL.
In order to evaluate the MQOs for precision, various analytical quality assurance/quality
control (QA/QC) samples were used, field measurement procedures were followed, and
field vouchers were collected. For analytical purposes, Method Detection Limits (MDL's)
were calculated for the detection of each analyte at low levels distinguished above
background noise, taking into consideration the relative sensitivity of an analytical
method, based on the combined factors of instrument signal, sample size, and sample
processing steps. The MDL is defined as "the minimum concentration of a substance
that can be measured and reported with 99% confidence that the analyte concentration
is greater than zero and is determined from analysis of a sample in a given matrix
containing the analyte." (Code of Federal Regulations 40 CFR Part 136). Approved
laboratories were expected to perform in general accord with the target MDLs presented
for NCA analytes (US EPA, 2001 a, Table A7-2). Because of analytical uncertainties
close to the MDL, there is greater confidence with concentrations above the Reporting
Limit (RL), which is the concentration of a substance in a matrix that can be reliably
quantified during routine laboratory operations. Typically, RLs are 3 to 5 times the MDL.
Concentrations between the MDL and the RL were used in generating the CDF and
42
-------
mean for the analyte. Values below the MDL were set to 0 and this value was used in
calculating both the CDFs and means.
Table 2-7 lists the units, method detection limits (MDL), and reporting limits (RL) for
each compound measured in sediment samples in all three states. The analytical
methods are those used in the NOAA NS&T Program (Lauenstein and Cantillo, 1993) or
documented in the EMAP-E Laboratory Methods Manual (U.S. EPA, 1993). The target
MDLs for the National Coastal Assessment (US EPA, 2001 a) were achieved in almost
90% of sediment analytes across the three states (Table 2-7). Exceedances of the
target MDL could potentially affect the frequency with which a compound is detected,
but would have little effect on the shape of the CDF since such exceedances occur at
the low end of the concentration distribution.
Table 2-8 lists the units, method detection limits (MDL), and reporting limit (RL) for the
tissue analytes. The target MDLs for the National Coastal Assessment (US EPA,
2001 a) were achieved in over 90% of tissue analytes across the three states (Table 2-
8). As mentioned for the sediments, exceedances of the target MDL could potentially
affect the frequency with which a compound is detected, but would have little effect on
the shape of the CDF since such exceedances occur at the low end of the concentration
distribution.
Prior to analysis of 1999 field samples, state laboratories participating in the NCA
program performed a demonstration of capability using SRMs provided by EPA.
Results of this exercise are described in EPA (2004, Appendix A). In summary, results
were deemed acceptable for Washington and California and marginal for Oregon.
A post-analysis assessment of the success of the analytical laboratories in meeting
NCA QA/QC guidelines was conducted by the QA officer of the Western Ecology
Division. These results are summarized in Table 2-9. Accuracy of results as assessed
by comparison to either an SRM, CRM, or LCM was within guidelines for all states for
analysis of metals in both sediment and tissues. For sediment PCBs and pesticides,
performance of the Oregon laboratory was less than the desired level, and the
performance of the California laboratories, while acceptable, was based on a limited
number of analytes in the LCM. For sediment PAHs, performance of the Oregon
laboratory was acceptable based on the LCM and less than desired based on the SRM.
In several cases, accuracy could not be assessed for the field samples because
laboratories did not analyze reference tissue material for PCBs (Washington) or
pesticides (Washington, California), although ability to meet standards was
demonstrated in the initial lab capability exercise.
The NCA analytical laboratory accuracy standards are based on the evaluation of
individual analytes (e.g. PCB congeners) while the NCA sediment condition indicators
are based on total sediment or tissue PAHs and PCBs. If the total PCB concentration in
the SRM is compared to the estimated total recovery of PCBs in sediments for all
congeners by the Oregon laboratory, the values are within 16% . A similar analysis for
43
-------
Table 2-7. Units, method detection limits (MDL), and reporting limits (RL) for sediment chemistry for compounds
measured in all three states. The method detection limits and the reporting limits for Oregon and Washington are means
of all the reported sediment values, including non-detects. Target MDLs are from the National Coastal Assessment (US
EPA, 2001 a). NR = not reported. NA = not applicable.
Analyte
Aluminum
Antimony
Arsenic
Cadmium
Chromium
Copper
Iron
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Tin
Units
(dry wt.)
M9/9
ug/g
ug/g
ug/g
ug/g
ug/g
ug/g
ug/g
ug/g
ug/g
ug/g
ug/g
ug/g
ug/g
Target
MDL
1500
0.2
1.5
0.05
5.0
5.0
500
1.0
1.0
0.01
1.0
0.1
0.05
0.1
CA
MDL/RL
0.05/0.15
0.002/0.006
0.1/0.3
0.002/0.006
0.03/0.09
0.03/0.09
2.0/6.0
0.002/0.006
0.003/0.009
0.015/0.045
0.006/0.018
0.002/0.006
0.008/0.024
0.002/0.006
OR
MDL/RL
1/4
0.3/1
0.3/1
0.03/0.09
0.06/0.2
0.2/0.6
0.8/2.5
0.2/0.7
0.1/0.3
0.002/0.007
0.3/1.0
0.09/0.3
0.0075/0.025
0.3/0.9
WA
MDL/RL
20/100
0.02/0.1
0.2/0.3
0.01/0.05
NR/0.5
0.5/1
20/100
0.01/0.2
0.2/1
0.001/0.005
1/1
0.1/0.1
0.1/0.2
0.02/0.1
-------
Zinc
PCB congeners
DDT, ODD, and DDE
PAHs
Aldrin
Alpha-Chlordane
Dieldrin
Endosulfan 1
Endosulfan II
Endosulfan Sulfate
Endrin
Heptachlor
Heptachlor Epoxide
Lindane
(gamma-BHC)
Mi rex
Trans-Nonachlor
TOO
Percent fines
ug/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
percent
percent
2.0
1.0
1.0
10
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
NA
NA
0.02/0.06
1/5
1/5
5/13
1/5
2/5
1/5
5/10
5/10
5/10
5/10
1/5
1/5
2/5
2/5
1/5
0.01/0.01
NR
0.3/0.9
0.87/1.10
0.01/0.92
2.65/30
0.01/0.92
0.01/0.92
0.1/0.92
0.1/0.92
0.1/0.92
0.02/1.70
0.1/0.92
0.1/0.92
0.1/0.92
0.1/0.92
0.1/0.92
0.1/0.92
0.0005/0.0005
0.1/1
1/1
0.06/0.59
0.06/0.61
1.1/1.1
0.06/0.59
0.06/0.59
0.06/0.59
0.06/0.59
0.06/0.59
0.06/0.59
0.06/0.59
0.06/0.59
0.06/0.60
0.060/0.63
0.06/0.59
0.05/0.59
0.1/0.1
0.1/0.1
-------
Table 2-8. Units, method detection limits (MDL), and reporting limits (RL) for tissue chemistry for compounds measured in
all three states. The reporting limits for Oregon and Washington are means of all the reported tissue values, including
non-detects. The reporting limits for the PCBs in Oregon and Washington are mean of all the congeners. The PCB
reporting limits in California are the range in individual congeners. Target MDLs are from the National Coastal
Assessment (US EPA, 2001 a). NA = not applicable.
Analyte
Aluminum
Arsenic
Cadmium
Chromium
Copper
Lead
Mercury
Nickel
Selenium
Silver
Zinc
PCB congeners
DDT, ODD, and DDE
Units
(wet wt.)
ug/g
ug/g
ug/g
ug/g
ug/g
ug/g
ug/g
ug/g
ug/g
ug/g
ug/g
ng/g
ng/g
Target
MDL
10.0
2.0
0.2
0.1
5.0
0.1
0.01
0.05
1.0
0.5
50.0
2.0
2.0
CA
MDL/RL
0.012/0.036
0.025/0.075
0.0005/0.0015
0.007/0.021
0.007/0.021
0.0005/0.0015
0.005/0.015
0.0015/0.0045
0.025/0.075
0.002/0.006
0.005/0.015
1/2-5
1/2
OR
MDL/RL
0.5/0.67
0.15/0.17
0.025/0.023
0.03/0.03
0.1/0.10
0.095/0.10
0.016/0.015
0.15/0.17
0.1/0.1
0.0085/0.0083
0.15/0.17
0.2-4.9/1.14
0.01/1.14
WA
MDL
2/10
0.2/1.5
0.01/0.05
0.1/0.2
0.5/0.5
0.01/0.05
0.01/3
0.5/0.5
0.1/0.3
0.01/0.01
1/1
0.1/0.41
0.1/0.51
-
O)
-------
Aldrin
Alpha-Chlordane
Dieldrin
Endosulfan 1
Endosulfan II
Endosulfan Sulfate
Endrin
Heptachlor
Heptachlor Epoxide
Lindane (gamma-BHC)
Mi rex
Toxaphene
Trans-Nonachlor
% Moisture
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
percent
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
NA
1/2
2/4
1/2
1/2
5/10
2/4
5/10
2/4
5/10
2/4
5/10
10/20
1/5
NA
0.01/1.14
0.01/1.14
0.01/1.14
0.01/1.14
0.01/1.14
0.02/2.25
0.01/1.14
0.01/1.14
0.01/1.14
0.01/1.14
0.01/1.14
0.01/11.4
0.01/1.14
NA
0.1/0.47
0.1/0.59
0.1/0.67
0.1/0.66
0.1/0.66
0.1/0.80
0.1/0.66
0.1/0.37
0.1/0.66
0.1/0.66
0.1/0.38
0.1/13.3
0.1/0.36
NA
-------
Table 2-9. Summary of performance of state analytical laboratories with regard to QA/QC criteria for analysis of reference
materials, matrix spike recoveries, and relative percent differences (RPD) of duplicates. MS = matrix spike, SRM =
Standard Reference Material, CRM = Certified Reference Material, LCM = Laboratory Reference Material, NA = not
analyzed.
Analyte Material state
CA
PAHs Sediment OR
WA
CA
Sediment OR
WA
Metals CA
Tissue OR
WA
CA
Sediment OR
PCBs WA
CA
Mean of all Less than 30% of analytes were within
analytes 35% of true value (% exceeding if >30%)
< ±30% SRM/CRM/LCM
(# analytes reported / # of analytes in
SRM/CRM/LCM)
Yes Yes LCM (15/22)
No No (44%) SRM 1 944 (1 8/1 9)
Yes Yes LCM (22/22)
Yes Yes SRM 1944(19/19)
Yes Yes LCM (14/1 5)
Yes Yes LCM (15/1 5)
Yes Yes LCM (14/1 5)
Yes Yes LCM (11/1 3)
Yes Yes LCM (13/1 3)
Yes Yes LCM (12/1 3)
Yes Yes LCM (13/21)
No No (76%) SRM 1 944 (1 9/1 9)
Yes Yes SRM 1944(17/19)
Yes* YesCRM(8*/21)
Matrix spike
recovery within
50%-150%
NoMSs
No
NoMSs
? - no true
values**
Yes
Yes
? - no true
values**
Yes
Yes
NoMSs
NoMSs
Yes
Yes
RPDs
MS / non-zero duplicate samples
average <30%
NA/Yes
No MS dups/Yes
NA/Yes
Yes/No sample dups
No MS dups/Yes
Yes/Yes
Yes/Yes
No MS dups/Yes
Yes/Yes
NA/no non-zeros
NA/No (low values)
Yes/No (low values)
Yes/Yes
00
-------
Tissue OR
WA
CA
Sediment OR
Pesticides WA
CA
Tissue OR
WA
Yes Yes LCM (21/21)
No no reference material used
Yes* Yes LCM (3*/20)
No NO (1 40%) SRM 1 944 (8/8)
Yes Yes SRM 1944 (8/8)
No no reference material used
Yes Yes LCM (20/20)
No no reference material used
Yes
Yes
NoMSs
Yes
Yes
Yes
Yes
Yes
No MS dups/Yes
Yes/Yes
NA/no non-zeros
No MS dups/Yes
Yes/No (low values)
Yes/No (low values)
No dups/Yes
Yes/Yes
* Fewer than 50% of NCA analytes were present in LCM.
** Duplicate values, but not true values, were reported for matrix spikes by the analytical laboratory.
CD
-------
the recovery of total PAHs in sediments versus the SRM by the Oregon lab was within
24%. These values are within ± 30% of the true value and are considered adequate for
the purpose of inclusion of the Oregon total PCB and total PAH data in the computation
of a regional CDF.
2.4.2 QA of Taxonomy
Quality control of taxonomic identifications involved the establishment of a network of
secondary QA/QC taxonomic specialists who confirmed identifications made by the
primary taxonomists (Table 2-10), and provided standardization of identifications among
the state participants.
In order to assure uniform taxonomy and nomenclature among the primary taxonomists
for each group, and to avoid problems with data standardization at the end of the
project, progressive QA/QC and standardization were implemented. At frequent,
regular intervals (i.e., monthly), as primary taxonomy was completed, vouchers, voucher
sheets, and a portion of the QA samples were sent to the QA taxonomists. Immediate
feedback from the QA taxonomists to the primary taxonomists was used to correct work
and standardize between regional taxonomists. Each voucher was accompanied by a
voucher sheet listing the following information: major taxon (e.g., Annelida), family,
genus, species, sample from which the specimen was taken; references used in the
identification; and any characteristics of the specimen that differ from the original
description. Provisional species were described in detail on the voucher sheet.
As voucher specimens and bulk samples were processed by the QA taxonomist, any
differences in identifications or counts were discussed and resolved with the primary
taxonomist. The original data set remained with the primary taxonomist, and changes
agreed upon between the primary and QA taxonomists were made by the primary
taxonomist on a copy of the original data set. Changes to the data based on QA/QC
analysis were tracked in writing by both the primary and QA taxonomists.
50
-------
Table 2-10. Listing of primary and QA/QC taxonomists by taxon and region for the 1999
Western Coastal EMAP study.
Organisms
Annelida
Arthropoda
Mollusca
Echinodermata
Miscellaneous taxa
Freshwater fauna
QA/QC
Taxon omist
Gene Ruff
Don Cadien
Don Cadien
Gordon Hendler
John Ljubenkov
Rob Plotnikoff/
Chad Wiseman
Primary
Taxonomists
John Oliver
Larry Lovell
Gene Ruff
Kathy Welch
Peter Slattery
Tony Phillips
Jeff Cordell
Peter Slattery
Kelvin Barwick
John Ljubenkov
Susan Weeks
Peter Slattery
Nancy Carder
Scott McEuen
Peter Slattery
John Ljubenkov
Scott McEuen
Not Applicable
Not Applicable
Jeff Cordell
Region*
NC
SC
WO
WO
NC
SC
WO
NC
NC
SC
WO
NC
SC
WO
NC
SC
WO
NC
SC
WO
*NC: Northern California, SC: Southern California, WO: Washington & Oregon
51
-------
2.5 Data management
Data management for the West Coast stations sampled in 1999 is a component of the
overall EMAP Western Coastal Information Management Program. The Information
Management System is based on a centralized data storage model using standardized
data transfer protocols (SDTP) for data exchange among program participants. The
1999 data were submitted to the Information Manager (IM) located at the Southern
California Coastal Water Research Program (SCCWRP) for entry into the relational
database (Microsoft Access 2000).
The data flow consists of interactions among four levels. Field crew leaders and
laboratory supervisors are responsible for compiling data generated by their
organizations and for entering the data into one or more of the SDTP tables. The State
IM Coordinator is responsible for compiling all data generated within a state into a unified
state database. The Western EMAP IM Coordinator (WIMC) is responsible for working
with State Coordinators to develop the SDTP, and for creation and management of the
centralized West Coast EMAP database. The EMAP IM Coordinator, located at the
Atlantic Ecology Division of EPA at Narragansett, Rhode Island, is responsible for
accepting data from Western EMAP, for placing it in the national EMAP database, and
for transferring it to other EPA databases, such as STORET.
Once all data tables of a particular data type (e.g., all tables containing fish data) were
certified by the WIMC, integrated multi-state data tables were provided to the Western
EMAP Quality Assurance Coordinator (QAC). The QAC reviewed the data with respect
to scientific content. Necessary corrections resulting from this review process were
returned to the Western EMAP IM Coordinator, who was responsible for working with the
State IM Coordinator to make necessary changes.
Following certification of all portions of the data by the QAC, the WIMC submitted the
integrated multi-state data set to the EMAP IM Coordinator, who is the point of contact
for data requests about the integrated data set.
Details of the Western EMAP Information Management process are provided in Cooper
(2000). The structure of each of the relational database tables and supporting database
look-up tables used by the states to submit data to the WIMC are also provided in this
document (Cooper, 2000).
2.6 Unsamplable Area
In Washington, 6 stations (WA99-0005, Ozette River; WA99-0028, Beardslee Slough;
WA99-0018, Quinault River; WA99-0032, WA99-0037, Willapa Bay; WA99-0041, Grays
River) proved to be inaccessible to sampling and were abandoned (Table 2-1).
In Oregon, station OR99-0029 was abandoned prior to sampling because inspection
found that it fell too far upstream and was not visited. Station OR99-0075, part of the
52
-------
Tillamook Bay intensification study, was not sampled because the station was located in
a marsh area. No sediment contaminant analyses were conducted at OR99-0044 or
OR99-0051 because of grab failures due to large amounts of rock and shell in the
substrate.
In California, all stations were visited. Among the base study stations, there were no grab
or trawl samples obtained at CA99-3019 (Carmel Bay) or CA99-3024 (San Luis Obispo
Bay) because of rocky substrate at the sites. Site CA99-3027, located in the Ventura
River, was not sampled because the station location was actually located on land and
the adjacent aquatic habitat could not be sampled because it consisted of a large
boulder substrate. Among the northern California intensification sites, no grab or trawl
samples were obtained at stations CA99-3058 (Klamath River), CA99-3066 (Noyo
River), CA99-3072 (Albion River), and CA99-3075 (Elk Creek) because of the presence
of rocky substrates. No trawl was obtained at station CA99-3056 (Wilson River)
because there was insufficient room to deploy gear.
53
-------
54
-------
3.0 Indicator Results
3.1 Habitat Indicators
3.1.1 Salinity
Salinity in the bottom water for the small estuaries of West Coast states ranged from 0
psu to 34.2 psu across the 201 stations where bottom salinities were collected.
Approximately fifty percent of the area of the small estuaries had a salinity > 30.9 psu
(Figure 3.1 -1). About 54% of the area of the West Coast states estuaries would be
classified as euhaline (> 30 psu) based on the EMAP sampling. The extended left tail of
the CDF indicates that a number of samples were taken at low salinities, but that these
sites constituted a modest percentage of the total estuarine area. Approximately 19% of
the area of the small estuaries had salinities less than 20 psu, while only 11 % of
estuarine area is represented by salinities less than 5 psu. The range of values for
surface salinity was identical to that in bottom water, and the CDF of surface salinity
values was very similar to that for bottom salinities. In interpreting these results, it is
important to recognize that salinity can vary both tidally and seasonally, as well as with
depth in the water column, and that these single measurements are "snapshots" during
the sampling events.
3.1.2 Water Temperature
Temperature in the bottom water for the small estuaries of West Coast states ranged
from 8.5 °C to 32.1 °C across the 201 stations where bottom temperatures were
collected. The relatively wide range of bottom water temperature values reflects the two
biogeographic provinces which were sampled in West Coast states. The range of
surface water temperatures was very similar to that for bottom water temperatures (9.3
°C to 32.1 °C). Approximately 13% of the area of the small estuaries had a temperature
at the bottom > 20 °C, with about 19.6 % of area having bottom water temperatures <
11.1 °C (Figure 3.1 -2). These temperatures are representative of summer conditions in
the region.
3.1.3 pH
The pH of bottom waters for the small estuaries of West Coast states had the
surprisingly wide range of from 5.1 to 10.2 across the 197 stations where bottom pH
measurements were collected. The range for pH in surface water samples was
identical to that for bottom waters. Approximately 91 % of the area of the small estuaries
had a pH < 8.0 (Figure 3.1 -3). Values of pH > 9 tended to be found at sites with low
salinity (< 7 psu), with the exception of the station from Point Mugu Lagoon, California,
where a pH of 9.3 and a salinity of 33.4 psu were recorded. Values of pH < 6.5 tended
to be found at sites with low salinity (< 1 psu).
55
-------
3.1.4 Sediment Characteristics
The percent silt-clay of sediments ranged from 0 % to 96.4 % at the 190 stations from
which soft sediment samples could be obtained (Figure 3.1 -4). About 65% of the area
of the small estuaries had sediments composed of sands (< 20 % silt-clay), about 29.4
% was composed of intermediate muddy sands (20-80 % silt-clay), and only about 5.6
% was composed of muds (>80 % silt-clay).
Percent total organic carbon (TOC) in sediments of small west coast estuaries ranged
from 0 % to 7.4 % at the 190 stations from which soft sediment samples could be
obtained (Figure 3.1 -5). About 84% of the area of the small estuaries had sediments
with TOC levels < 1.0%.
3.1.5 Water Quality Parameters
Water quality parameters are presented as water column mean values based on the
concentration averaged over the surface, mid-water, and bottom water samples. Water
depths during sampling ranged between 0.3 m and 30 m depth.
Chlorophyll a
The average water column concentration of chlorophyll a of small west coast estuaries
(Figure 3.1 -6) ranged from 0.4 to 47.6 ug L"1 across the 202 stations where chlorophyll
measurements were collected. Approximately 88% of total estuarine area was
characterized by average chlorophyll a concentrations < 7.9 ug L"1, while approximately
0.6 % of estuarine area had chlorophyll a values that exceeded concentrations of 15 ug
L"1. There was no geographic concentration of high chlorophyll values.
Nutrients
The average water column concentration of nitrate + nitrite of small west coast estuaries
(Figure 3.1 -7) ranged from 0 to 3472 ug L"1 across the 202 stations where nitrate +
nitrite measurements were collected. Approximately 95% of total estuarine area was
characterized by nitrate + nitrite concentrations < 263 ug L"1, while approximately 2.7 %
of estuarine area had nitrate + nitrite values that exceeded concentrations of 300 ug L"1.
The average water column concentration of ammonium in small west coast estuaries
(Figure 3.1 -8) ranged from 0 to 580 ug L"1 across the 202 stations where ammonium
measurements were collected. Approximately 90% of total estuarine area was
characterized by ammonium concentrations < 125 ug L"1.
The average water column concentration of total nitrogen (nitrate + nitrite + ammonium)
in small west coast estuaries (Figure 3.1 -9) ranged from 3.2 to 3519 ug L"1 across the
202 stations where total nitrogen measurements were collected. Approximately 90% of
total estuarine area was characterized by total nitrogen concentrations < 218 ug L"1.
56
-------
The average water column orthophosphate concentration of small west coast estuaries
(Figure 3.1 -10) ranged from 0 to 563.3 ug L"1 across the 202 stations where
orthophosphate measurements were collected. Approximately 95% of total estuarine
area was characterized by orthophosphate concentrations < 158 ug L"1.
The ratio of total nitrogen (nitrate + nitrite + ammonium) concentration to total
orthophosphate concentration was calculated as an indicator of which nutrient may be
controlling primary production in west coast small estuaries. A ratio above 16 is
generally considered indicative of phosphorus limitation, and a ratio below 16 is
indicative of nitrogen limitation (Geider and La Roche, 2002). The N/P ratio (Figure 3.1
-11) ranged from 0.16 to 393.5 across the 190 stations where sufficient measurements
were collected. Approximately 75% of estuarine area had N/P values < 16. The long
right tail of the CDF was due to four stations representing less than 1 % of estuarine
area with N/P ratios > 100.
Total Suspended Solids
The average water column concentrations of total suspended solids (TSS) in the water
column of small west coast estuaries (Figure 3.1-12) ranged from 0 to 276.2 mg L1
across the 201 stations where TSS measurements were collected. Approximately
95% of total estuarine area was characterized by TSS concentrations < 19.1 mg L1.
Percent Light Transmission
The percent light transmission of the water column (adjusted to a reference sample
depth of 1 m) in small west coast estuaries (Figure 3.1 -13) ranged from 0 to 87.6% of
surface illumination. Approximately 21.3 % of total estuarine area showed a percent
light transmission of <10 %, and approximately 46.8 % of total estuarine area showed a
percent light transmission of <20 %.
3.1.6 Water Column Stratification
As an indicator of water column stratification, two indices were calculated for the 201
stations with temperature and salinity data. The first index was the simple difference
between bottom and surface salinities. The second index (Aot) was the difference
between the computed bottom and surface ot values, where ot is the density of a parcel
of water with a given salinity and tmperature relative to atmospheric pressure. Results
of the two indices were extremely similar.
The simple stratification index ranged between -1.2 and 20.2 psu. Less than 4% of
estuarine area showed index values < 0, indicating bottom waters less saline than
surface waters (Figure 3.1 -14). Approximately 12% of estuarine area had index values
> 2 psu, indicating strong stratification. The Aot index had values ranging from -0.08 to
+16.2. Approximately 3% of estuarine area showed Aot index values < 0, indicating
57
-------
bottom waters less saline than surface waters (Figure 3.1 -15). Approximately 12% of
estuarine area had Aot index values > 2, indicating strong stratification.
The limited indication of strong water column stratification within the small west coast
estuaries sampled is consistent with the large tidal amplitude across much of the region,
which should lead to a high degree of water column mixing. Additionally the sampling
period is during the summer period of low rainfall and low freshwater runoff which
should also reduce the extent of vertical stratification during the sample period.
Bottom Salinity
West Coast Small Estuaries
100-
TO
80
0)
o
Q_
I 40
D
O
20-
- Cumulative Percent
• 95% Confidence Interval
10 15 20 25
Salinity (psu)
30
35
40
Figure 3.1-1. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. salinity of bottom waters.
58
-------
100
as
£ 80
<
+J
-------
Bottom pH
West Coast Small Estuaries
(0
L.
<
+-i
0)
-------
Percent Sediment Silt-Clay
West Coast Small Estuaries
- - - - . 95% Confidence Interval
0
20 40 60
Silt-Clay (%)
80 1C
Figure 3.1-4. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. percent silt-clay of sediments.
61
-------
re
0)
£
0)
Q_
0)
?
_re
3
E
.2 40
o
20
Percent Sediment Total Organic Carbon
West Coast Small Estuaries
100-
- Cumulative Percent
•95% Confidence Interval
23456
Total Organic Carbon (%)
Figure 3.1-5. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. percent total organic carbon of sediments.
62
-------
Mean Chlorophyll a Concentration
West Coast Small Estuaries
100
S3 80
0)
o
60 -
0)
0.
0)
I 40
20 -
•Cumulative Percent
- - • 95% Confidence Interval
10 20 30
Concentration (ug/L)
40
50
Figure 3.1-6. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. water column mean concentration of chlorophyll a.
63
-------
Mean Nitrate+Nitrite Nitrogen Concentration
West Coast Small Estuaries
-Cumulative Percent
. . . . .95% Confidence Interval
500 1000 1500 2000 2500
Concentration (ug/L)
3000
3500
4000
Figure 3.1-7. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. water column mean nitrate + nitrite concentration.
64
-------
Mean Ammonium Nitrogen Concentration
West Coast Small Estuaries
100 -
ra
£ 80
0)
60 -
0)
Q.
I
« 40
3
E
3
o
20 -
Cumulative Percent
.95% Confidence Interval
50 100 150 200 250
Concentration (ug/L)
300
350
400
Figure 3.1-8. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. water column mean ammonium concentration.
65
-------
Mean Total Dissolved Nitrogen Concentration
West Coast Small Estuaries
- -
- - .95%
ulative Percent
Confidence Interval
500 1000 1500 2000 2500
Concentration (ug/L)
3000
3500
4000
Figure 3.1-9. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. water column mean total nitrogen (nitrate + nitrite + ammonium) concentration.
66
-------
Mean Orthophosphate Phosphorus Concentration
West Coast Small Estuaries
100-
80
60
I
'*J
I 40
E
3
o
20-
50
- - .95% Confidence Interval
100 150
Concentration (ug/L)
200
250
Figure 3.1-10. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. water column mean orthophosphate concentration.
67
-------
Mean N:P Molar Ratio
West Coast Small Estuaries
100-
- Cumulative Percent
•95% Confidence Interval
100
150
200 250
Molar Ratio
300
350
400
450
Figure 3.1-11. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. water column mean ratio of total nitrogen (nitrate + nitrite + ammonium)
concentration to total orthophosphate concentration.
68
-------
Mean Total Suspended Solids
West Coast Small Estuaries
100-
re
80-
60-
40
E
3
o
20-
• Cumulative Percent
- - - - • 95% Confidence Interval
50 100 150 200
Concentration (mg/L)
250
300
Figure 3.1-12. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. water column total suspended solids concentration.
69
-------
Percent Light Transmission at 1 m
West Coast Small Estuaries
100
re
80
0)
e
a, 60
o>
'^
_re
= 40
E
o
20
Cumuladve Percent
95% Confidence Interval
10 20 30 40 50 60 70
Percent Light Transmission
80 90
100
Figure 3.1-13. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. percent light transmission estimated at a reference depth of 1 m in the water
column.
70
-------
Stratification Index
West Coast Small Estuaries
100-
re
80-
g 60
40
E
3
o
20-
-5
Cumulative Percent
- - - - • 95% Confidence Interval
0 5 10 15
Bottom Salinity Minus Surface Salinity
20
25
Figure 3.1-14. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. water column stratification index.
71
-------
Aat
West Coast Small Estuaries
100
80
0)
60
0)
?
| 40
3
O
20 -
-2
•Cumulative Percent
.... -95% Confidence Interval
4 6 8 10 12
(at bottom - at surface)
14
16
18
Figure 3.1-15. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. Aot stratification index.
72
-------
3.2 Exposure Indicators
3.2.1 Dissolved Oxygen
Dissolved oxygen (DO) concentrations in the bottom water for the small estuaries of West
Coast states ranged from 3.75 mg L"1 to 16.3 mg L"1 across the 200 stations where
dissolved oxygen concentrations were measured. No observations were less than the
value of 2 mg L"1 considered indicative of anoxia, less than four percent of estuarine area
had a bottom DO concentration below 5 mg L"1, and approximately 92% of the area of
West Coast small estuaries had DO concentrations between 5 and 10 mg L"1 ( Fig. 3.2-1).
The range of dissolved oxygen (DO) concentrations in the surface waters was very similar
to that for bottom waters (3.46 mg L1 to 16.3 mg L1) (Fig. 3.2-2). Approximately 83% of
the area of West Coast small estuaries had surface DO concentrations between 5 and 10
mg L"1, while nearly 11 % had DO concentrations > 10 mg/L"1.
3.2.2 Sediment Contaminants
3.2.2.1 Sediment Metals
Concentrations of metals in sediment were measured at 190 stations, except antimony
and silver, which were measured at only 189 stations. The mean concentration of a metal
was calculated using all available samples with the non-detects set to 0. For comparative
purposes, mean concentrations of metals were also calculated using the subset of
samples in which the metals were detected (Table 3.2-1).
Arsenic
Arsenic was detected in 189 of the stations and had a mean concentration of 6.11 ug/g
(Table 3.2-1). The maximum concentration of 18.6 ug/g occurred in Grays Bay in the
Columbia River, Washington. The next two highest concentrations of 17.6 and 17.1 ug/g
occurred in Tillamook Bay, Oregon, and the Los Angeles Harbor, respectively. Fifty
percent of the area of the West Coast small estuaries had concentrations less than 5.53
ug/g, and 90% of the area had concentrations less than 8.75 ug/g (Figure 3.2-3). Arsenic
concentrations exceeded the ERL at 37 stations (14.8% of area), while no stations had
values exceeding the ERM (Table 3.2-1).
Cadmium
Cadmium was detected in 164 of the stations and had a mean concentration of 0.219
ug/g (Table 3.2-1). The maximum concentration of 4.30 ug/g occurred in the Los Angeles
Harbor. The only other value >1 ug/g was the 2.3 ug/g concentration in Discovery Bay,
which opens into the Strait of Juan de Fuca, Washington. Fifty percent of the area of the
West Coast small estuaries had cadmium concentrations less than 0.15 ug/g, and 90% of
the area had concentrations less than 0.44 ug/g (Figure 3.2-4). Cadmium concentrations
exceeded the ERL at only 2 stations (0.1% of area), while no stations had values
exceeding the ERM (Table 3.2-1).
73
-------
Bottom Dissolved Oxygen
West Coast Small Estuaries
ra
0)
0)
u
0)
Q.
0)
?
ra
E
o
- - - - • 95% Confidence Interval
4 6 8 10 12
Concentration (mg/L)
14
16
18
Figure 3.2-1. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. dissolved oxygen of bottom waters.
74
-------
Surface Dissolved Oxygen
West Coast Small Estuaries
100-
80 -
0)
0)
60 -
1 40
O
20 -
Cumulative Percent
95% Confidence Interval
6 8 10 12 14
Concentration (mg/L)
16 18
Figure 3.2-2. Percent area (and 95% C.I.) of small estuaries of the West Coast states
vs. dissolved oxygen of surface waters.
75
-------
Chromium
Chromium was detected at all 190 stations and had a mean concentration of 128 ug/g
(Table 3.2-1). The two highest concentrations of 1770 and 1250 ug/g both occurred in
the Smith River, California. These were the only concentrations >1000 ug/g. Fifty
percent of the area of the West Coast small estuaries had concentrations less than 48.6
ug/g, and 90% of the area had concentrations less than 168 ug/g (Figure 3.2 -5).
Chromium concentrations exceeded the ERL at 68 stations (27% of area), while 10
stations (2.5% of area) had values exceeding the ERM (Table 3.2-1).
Copper
Copper was detected at all 190 stations and had a mean concentration of 26.7 ug/g
(Table 3.2-1). The maximum concentration of 398 occurred in the Los Angeles Harbor.
The only other value >100 ug/g was the 156 ug/g value in Santa Barbara Harbor,
California. Fifty percent of the area of the West Coast small estuaries had
concentrations less than 14.5 ug/g, and 90% had concentrations less than 55.2 ug/g
(Figure 3.2-6). Copper concentrations exceeded the ERL at 54 stations (21.2% of
area), while 1 stations (0.1% of area) had a value exceeding the ERM (Table 3.2-1).
Lead
Lead was detected at all 190 stations and had mean concentration of 13.6 ug/g
(Table 3.2-1). The maximum concentration of 293 ug/g occurred in the Los Angeles
Harbor, and the second highest value of 80 ug/g occurred in Santa Barbara Harbor,
California. Fifty percent of the area of the small estuaries had lead concentrations less
than 8.87 ug/g, and 90% of the area had concentrations less than 20.4 ug/g
(Figure 3.2-7). Lead concentrations exceeded the ERL at only 5 stations (1.3% of
area), while 1 station (0.07% of area) had a value exceeding the ERM (Table 3.2-1).
Mercury
Mercury was detected at 180 of the stations and had a mean concentration of 0.113
ug/g (Table 3.2-1). The maximum concentration of 3.11 ug/g occurred in the Estero
Americano, California. The only other values >1 ug/g occurred in the Los Angeles
Harbor and the Albion River, California, which had concentrations of 2.33 and 1.37 ug/g,
respectively. Fifty percent of the area of the West Coast small estuaries had mercury
concentrations less than 0.03 ug/g, and 90% of the area had concentrations less than
0.16 ug/g (Figure 3.2-8). Mercury concentrations exceeded the ERL at 25 stations
(12.1% of area), while 3 stations (0.1% of area) had values exceeding the ERM (Table
3.2-1).
Nickel
Nickel was detected at all 190 stations and had a mean concentration of 47.6 ug/g
(Table 3.2-1). The two highest concentrations, 354 ug/g and 307 ug/g, both occurred in
the Smith River, California. Fifty percent of the area of the West Coast small estuaries
had nickel concentrations less than 18.6 ug/g, while 90% of the area had concentrations
less than 50.0 ug/g (Figure 3.2-9). Nickel concentrations exceeded the ERL at 116
76
-------
stations (43.7% of area), while 45 stations (9.4% of area) had values exceeding the
ERM (Table 3.2-1). Nickel concentrations in relation to the published ERM values
should be interpreted cautiously since the ERM value has a low reliability (Long et al.,
1995). Because of its unreliability, nickel was excluded from a recent evaluation of
sediment quality in southern Puget Sound (Long et al., 2000). Additionally, a study of
metal concentrations in cores on the West Coast determined an historical background
concentration of nickel in the range of 35 - 70 ppm (Lauenstein et al., 2000), which
brackets the value of the ERM (51.6 ppm).
Selenium
Selenium was detected at 78 of the stations and had a mean concentration of 0.107
ug/g (Table 3.2-1). The maximum concentration of 1.6 ug/g occurred in the Los
Angeles Harbor. Of the seven other values >0.5 ug/g, six occurred in California and
one in Oregon. Approximately 71 % of the area of the West Coast small estuaries had
non-detectable levels of selenium, and 90% had concentrations less than 0.25 ug/g
(Figure 3.2-10). No stations exceeded either the ERL or ERM for selenium.
Silver
Silver was detected at 178 of the stations and had a mean concentration of 0.16 ug/g
(Table 3.2-1). The maximum concentration of 1.13 ug/g occurred in the Los Angeles
Harbor. The second and third highest values of 0.98 and 0.92 ug/g were found in
Grays Bay, Washington, and San Diego Bay, respectively. Fifty percent of the area of
the West Coast small estuaries had a silver concentrations less than 0.21 ug/g, while
90% of the area had concentrations less than 0.48 ug/g (Figure 3.2-11). Silver
concentrations exceeded the ERL at only 1 station (0.1% of area) (Table 3.2-1), and no
stations exceeded the ERM.
Tin
Tin was detected at 130 stations and had a mean concentration of 1.24 ug/g
(Table 3.2-1). The maximum concentration of 17.3 ug/g occurred in the Los Angeles
Harbor. The only other value greater than 10 ug/g was in the Albion River, California,
which had a concentration of 11.6 ug/g. Fifty percent of the area of the West Coast
small estuaries had a tin concentration less than 0.99 ug/g, while 90% of the area had
concentrations less than 2.67 ug/g (Figure 3.2-12).
Zinc
Zinc was detected at all 190 stations and had a mean concentration of 69.5 ug/g
(Table 3.2-1). The maximum concentration of 538 ug/g occurred in the Los Angeles
Harbor, while the next highest value, 173 ug/g, was found in both the Santa Barbara
Harbor and San Diego Bay. Fifty percent of the area of the West Coast small estuaries
had zinc concentrations less than 49 ug/g, while 90% of the area had concentrations
less than 117 ug/g (Figure 3.2-13). Zinc concentrations exceeded the ERL at 4 stations
(1.2% of area), while 1 station (0.1% of area) had a value exceeding the ERM (Table
3.2-1).
77
-------
Additional Metals
In addition to the 11 metals discussed above, aluminum, antimony, iron, and
manganese were measured in the sediments. The measured concentration and
frequency of detection for each of these metals are given in Table 3.2 -1. Each of these
four metals was detected at all of the stations, with the exception of antimony, which
was detected at 115 stations. Not unexpectedly, aluminum and iron were the two most
abundant metals, with mean concentrations of 44631 ug/g and 33642 ug/g,
respectively.
78
-------
Table 3.2-1. Summary statistics for sediment metal concentrations (ug/g) for all stations from West Coast estuaries. The
overall mean and the overall standard deviation (SD) were calculated using all the data, including the non-detects which
were set to 0. (N = 190, except 189 for antimony and silver). The "mean when present" was calculated using the samples
which had detectable concentrations of the compound. ERL and ERM values are from Long et al. (1995).
Metal
Aluminum
Antimony
Arsenic
Cadmium
Chromium
Copper
Iron
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Tin
Zinc
Overall
Mean
Concen-
tration
44631
0.432
6.11
0.219
128
26.7
33600
13.6
485
0.113
47.6
0.107
0.16
1.24
69.5
Overall
SD
19837
1.24
3.05
0.38
209
34.8
18600
22.7
278
0.302
55.4
0.209
0.20
1.86
52.0
Mean
Concen
-tration
when
Present
44631
0.71
6.14
0.254
128
26.7
33600
13.6
485
0.120
47.6
0.261
0.17
1.81
69.5
Min
3030
0
0
0
9.2
2.1
6000
3.0
84.8
0
3.3
0
0
0
7.9
Max
78800
16.4
18.6
4.3
1770
398
87500
293
1390
3.11
354
1.60
1.13
17.3
538
Frequency
of
detection
190
115
189
164
190
190
190
190
190
180
190
78
178
130
190
ERL
8.2
1.2
81
34
46.7
0.15
20.9*
2.0
1.0
150
ERM
70.0
9.6
370
270
218.
0.71
51.6*
25.0
3.7
410
>ERL
No.
Sites
37
2
68
54
5
25
116*
0
1
4
>ERM
No.
Sites
0
0
10
1
1
3
45*
0
0
1
>ERL
Area
14.8
0.1
27
21.2
1.3
12.1
43.7*
0
0.1
1.2
>ERM
Area
0
0
2.5
0.01
0.07
0.1
9.4*
0
0
0.1
* The ERL and ERM for nickel has low reliability for the West Coast. See text for discussion.
-------
Sediment Arsenic Concentration
West Coast Small Estuaries
100-
re
g> 80
60
I
^ 40
E
3
o
20-
Cumulative Percent
- - - .95% Confidence Interval
5 10 15
Concentration (ug/g)
20
Figure 3.2-3. Percent area (and 95% C.I.) of West Coast small estuaries vs. sediment
concentration of arsenic.
80
-------
o
Sediment Cadmium Concentration
West Coast Small Estuaries
100 -
TO 80
a>
0)
a eo H
0)
D.
0)
^
* 40
20-
•Cumualtive Percent
- - - - '95% Confidence Interval
2 3
Concentration (ug/g)
Figure 3.2-4. Percent area (and 95% C.I.) of West Coast small estuaries vs. sediment
concentration of cadmium.
81
-------
Sediment Chromium Concentration
West Coast Small Estuaries
- - - - • 95% Confidence Interval
500 1000 1500
Concentration (ug/g)
2000
Figure 3.2-5. Percent area (and 95% C.I.) of West Coast small estuaries vs. sediment
concentration of chromium.
82
-------
Sediment Copper Concentration
West Coast Small Estuaries
100-
Cumulative Percent
- - '95% Confidence Interval
100 200 300
Concentration (ug/g)
400
500
Figure 3.2-6. Percent area (and 95% C.I.) of West Coast small estuaries vs. sediment
concentration of copper.
83
-------
Sediment Lead Concentration
West Coast Small Estuaries
100-
S 80
k.
<
•+•»
^ 60-
(i)
D.
0)
| 40-
E
3
o
20-
•Cumulative Percent
- - - - '95% Confidence Interval
50 100 150 200 250
Concentration (ug/g)
300
350
Figure 3.2-7. Percent area (and 95% C.I.) of West Coast small estuaries vs. sediment
concentration of lead.
84
-------
Sediment Total Mercury Concentration
West Coast Small Estuaries
— Cumulative Percent
- • 95% Confidence Interval
0.5 1 1.5 2 2.5
Concentration (ug/g)
3.5
Figure 3.2-8. Percent area (and 95% C.I.) of West Coast small estuaries vs. sediment
concentration of mercury.
85
-------
Sediment Nickel Concentration
West Coast Small Estuaries
100 -
as
£ 80
0)
5 60
Q.
-------
Sediment Selenium Concentration
West Coast Small Estuaries
100 -
-------
Sediment Silver Concentration
West Coast Small Estuaries
100 -
g) 80
60
0)
^ 40
E
3
o
20 -
Cumulative Percent
. . . . .95% Confidence Interval
0.2 0.4 0.6 0.8
Concentration (ug/g)
1.2
Figure 3.2-11. Percent area (and 95% C.I.) of West Coast small estuaries vs. sediment
concentration of silver.
88
-------
Sediment Tin Concentration
West Coast Small Estuaries
100-
re
g> 80
! 60
0.
-------
Sediment Zinc Concentration
West Coast Small Estuaries
100
TO 80 -
0)
<
•+•»
y 60-
0)
D.
0)
1 40
E
3
o
20-
Cumulative Percent
- - - - '95% Confidence Interval
100 200 300 400
Concentration (ug/g)
500
600
Figure 3.2-13. Percent area (and 95% C.I.) of West Coast small estuaries vs. sediment
concentration of zinc.
90
-------
3.2.2.2 Sediment Organics
An overall mean concentration was calculated for sediment organics using all the
samples (N=190) with the non-detects set to 0. "Mean concentrations when present"
were also calculated using the subset of samples in which the compounds were
detected (Table 3.2-2)
Total PAHs
PAHs were detected at 112 of the stations. One laboratory replicate from a sediment
sample from Martin Slough in the Columbia River had individual PAH concentrations 3
to 690 times greater than in the other three replicates from the same sample. Total
PAH concentration for this sample was 59,878 ng/g if the high laboratory replicate was
included, but 2427 ng/g if it was excluded. The order-of-magnitude higher
concentrations in this replicate could be due to a drop of creosote. Because the sample
appears to be an outlier relative to the other laboratory replicates at the station, this
sample was not included in the total PAH analysis.
Total PAHs had an overall mean concentration of 263 ng/g dry weight (Table 3.2-2).
The highest concentration, 22,982 ng/g, occurred in the Los Angeles Harbor. The
compounds 2,6-Dimethylnaphthalene, 2,3,5-Trimethylnaphthalene, and
1-Methylphenanthrene constituted 61% of the total PAHs at the Los Angeles Harbor
site. Fifty percent of the area of the West Coast small estuaries had a total PAH
concentration less than 25 ng/g, and 90% of the area had a concentration less than 435
ng/g (Figure 3.2-14). On the average, low molecular weight (LMW) PAHs constituted
57 % of the total PAHs, while high molecular weight (HMW) PAHs constituted 43 % of
the total PAHs (Table 3.2-2). Four stations exceeded the ERL for both HMW (0.2 % of
area; Figure 3.2-15) and LMW PAHs (0.9 % of area; Figure 3.2-16), and two stations
exceeded the ERL (0.2 % of area) for total PAHs. The ERM was exceeded only for
LMW PAHs at two stations (Table 3.2-2).
Total PCBs
PCBs were detected at 78 of the stations, and total PCBs had an overall mean
concentration of 3.72 ng/g dry weight (Table 3.2-2). The maximum concentration of
86.5 ng/g dry weight occurred in San Diego Bay, while the second highest concentration
of 66.2 ng/g occurred in the Los Angeles Harbor. Seventy-three percent of the area of
the West Coast small estuaries had non-detectable levels of PCBs, while 90% of the
area had concentrations less than 7.5 ng/g (Figure 3.2-17). PCB18 was the most
abundant PCB conger and made up 18% of the total PCBs on average. The next most
abundant congener was PCB52, which made up 11 % of the total PCBs. PCB18 and
PCB52 were also the most frequently detected PCB congeners, occurring in 69 and 68
of the stations, respectively. The ERL for total PCBs was exceeded at 7 stations (2.2%
of area), while no stations exceeded the ERM (Table 3.2-2).
91
-------
Total DDT
DDT or one of its metabolites was detected at 28 of the stations, including 13 in
California, 3 in Oregon and 9 in Washington. Total DDT had an overall mean
concentration of 3.29 and a maximum concentration of 301 ng/g dry weight in the
Channel Island Harbor in Southern California (Table 3.2-2). The only two other values
>50 ng/g were the 99 and 50 ng/g concentrations in the Long Beach Harbor and the Los
Angeles Harbor, respectively. Eighty-eight percent of the area of the small estuaries
had non-detectable levels of DDTs, while 90% of the area had total DDT concentrations
less than 0.31 ng/g (Figure 3.2-18). The most abundant form was 4,4'-DDD,
constituting 77% of the total DDT on average (Table 3.2-2). The concentration of 4,4'-
DDD exceeded the ERL at 15 stations (6.1% of area), and exceeded the ERM at 3
stations (1.6% of area) (Table 3.2-2). The ERL for total DDT was exceeded at 17
stations (6.2% of area), while the ERM was exceeded at 3 stations (0.1% of area)
(Table 3.2-2).
Additional Pesticides
Besides DDT, an additional 12 pesticides were measured in the sediments in all three
states (Table 3.2-2). Of these Dieldrin, Endosulfan II and Mirex were never detected at
any station. The other pesticides occurred in 3 to 11 of the 190 sediment samples. An
overall mean concentration was calculated for each of these pesticides using all the
samples (N=190) with the non-detects set to 0. Because of their low frequency of
detection, means were also calculated for these pesticides using just the samples in
which the pesticides were detected. Endrin had the highest concentrations, with an
overall mean concentration of 0.36 ng/g and a mean of 7.50 ng/g at the sites where it
was detected. All nine sites where endrin was detected had concentrations which
exceeded the ERL but not the ERM. Trans-nonachlor was the second most abundant of
the additional pesticides, with an overall mean of 0.21 ng/g and a mean of 5.70 ng/g
where detected. There was an insufficient number of detects to calculate CDFs for any
of the additional pesticides.
92
-------
Table 3.2-2. Mean sediment concentrations (ng/g dry weight) and frequency of detection of the PAHs, PCBs and pesticides
measured in all three states. The overall mean and the overall standard deviation (SD) were calculated using all the data including
the non-detects, which were set to 0. The "mean when present" was calculated using the samples which had detectable
concentrations of the compound. N = 190. ERL and ERM values are from Long et al. (1995). NA - not analyzed, see text.
Analyte Overall mean Overall Mean Min
concentration SD concentration
ng/g dry wt when
present
HMW PAHs
LMW PAHs
Total PAHs
Total PCBs
2,4'-DDD
2,4'-DDE
2,4'-DDT
4,4'-DDD
4,4'-DDE
4,4'-DDT
Total DDT
Aldrin
Alpha-chlordane
Dieldrin
Endosulfan I
Endosulfan II
Endosulfan
Sulfate
Endrin
Heptachlor
Heptachlor
Epoxide
Lindane
(gamma-BHC)
Mi rex
Trans-nonachlor
112
151
263
3.72
0.089
0.183
0.190
0.285
2.53
0.015
3.29
0.022
0.067
0.000
0.020
0.000
0.053
0.355
0.131
0.053
0.005
0.000
0.210
371.2
1460
1700
9.57
0.79
1.20
2.62
2.12
17.7
0.20
23.6
0.22
0.42
0.00
0.28
0.00
0.40
1.60
0.58
0.54
0.07
0.00
1.31
199
398
446
9.05
4.21
4.97
36.1
5.42
17.1
2.80
22.3
1.38
2.54
0.000
3.80
0.00
2.54
7.50
2.26
5.00
1.00
0.00
5.70
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Max Frequency ERL ERM >ERL
of
detection No. Sites
2918
20064
22982
86.5
9.20
13.6
36.1
26.7
224
2.80
301
2.90
3.50
0.00
3.80
0.00
3.60
7.50
3.70
6.70
1.00
0.00
12.7
107 1700 9600 4
72 552 3160 4
112 4022 44792 2
78 22.7 180 7
4
7
1
10
28 2.2 27.0 15
1
28 1.58 46.1 17
3
5
0 0.02 8 0
1
0
4
9 0.02 45 9
11
2
1
0
7
>ERM >ERL >ERM
No. Sites Area % Area %
0 0.2 0
2 0.9 0.1
0 0.2 0
0 2.2 0
3 6.1 1.6
3 6.2 0.1
0 NA NA
0 NA NA
-------
Sediment Total PAHs
West Coast Small Estuaries
100
TO
0)
0)
0)
Q_
0)
80
y 60
5 40
E
3
o
20-
• Cumulative Percent
- • 95% Confidence Interval
5000
10000 15000
Concentration (ng/g)
20000
25000
Figure 3.2-14. Percent area (and 95% C.I.) of West Coast small estuaries vs. sediment
concentration of total PAHs.
94
-------
Sediment High Molecular Weight PAHs
West Coast Small Estuaries
20
- Cumulative Percent
95% Confidence Interval
500 1000 1500 2000
Concentration (ng/g)
2500
3000
3500
Figure 3.2-15. Percent area (and 95% C.I.) of West Coast small estuaries vs. sediment
concentration of high molecular weight PAHs.
95
-------
Sediment Low Molecular Weight PAHs
West Coast Small Estuaries
100
c
0)
g 60
0)
5 40
|
o
20-
• Cumulative Percent
• 95% Confidence Interval
5000
10000 15000
Concentration (ng/g)
20000
25000
Figure 3.2-16. Percent area (and 95% C.I.) of West Coast small estuaries vs. sediment
concentration of low molecular weight PAHs.
96
-------
Sediment Total PCBs
West Coast Small Estuaries
100-
80-
0)
o>
a.
60-
3 40-
E
o
20-
• Cumulative Percent
•95% Confidence Interval
10 20 30 40 50 60
Concentration (ng/g)
70
80
90
100
Figure 3.2-17. Percent area (and 95% C.I.) of West Coast small estuaries vs. sediment
concentration of total PCBs.
97
-------
Sediment Total DDT Concentration
West Coast Small Estuaries
100 -
S 80
60
0)
40
|
O
20 -
Cumulative Percent
- - - - '95% Confidence Interval
50 100 150 200 250
Concentration (ng/g)
300
350
Figure 3.2-18. Percent area (and 95% C.I.) of West Coast small estuaries vs. sediment
concentration of total DDT.
98
-------
3.2.3 Sediment Toxicity
3.2.3.1 Ampelisca abdita
Sediment toxicity tests with the amphipod Ampelisca abdita were conducted on a total
of 190 sediment samples, 41 in Washington, 76 in Oregon, and 73 in California. Control
conditions for a successful toxicity test with this species require a mean of 90% survival
in the five replicates in control sediments, with no replicate less than 80%. If the
amphipods do not survive at acceptable levels in control replicates, it may be possible
that they were unduly stressed due to shipping or laboratory holding conditions and that
their response to test sediments may be compromised. The quality control requirements
were not met in 24 of the 190 samples, and these samples were excluded from the CDF
analysis, leaving 166 samples for analysis. The stations that were excluded included 7
in Washington, 6 in Oregon and 11 in California.
The control-corrected survivorship of Ampelisca abdita in bioassays of sediments
collected in West Coast small estuaries (Figure 3.2 -19) ranged from 0 % to 109.9 %
across the 166 stations that were included in the analysis. Approximately 9.2 % of the
area of West Coast small estuaries (represented by 12 sites) had control-corrected
survivorship of Ampelisca abdita in sediment bioassays < 80%. Over 19 % of area had
control-corrected survivorship > 100 %, indicating better survival of amphipods in test
sediments than in controls.
Four stations in Washington, one in Oregon and seven stations in California had mean
survival in test sediments less than 80%. Only four stations had mean survival in test
sediments less than 60%; these included two sites in the Smith River, one site in the
Los Angeles River in California, and one site in Grays Bay, Washington. Of the 12 sites
with survival less than 80%, five sites showed evidence of high levels of sediment
contaminants.
3.2.3.2 Arbacia punctulata
Sediment porewater toxicity tests with sea urchins, Arbacia punctulata, were conducted
on 41 sites in Washington, 36 base stations in Oregon, and 47 base stations in
California, for a total of 124 samples. No sediments from the intensification sites in
northern California or Tillamook Bay, Oregon, were tested with Arbacia. Five test
sediments from Oregon (OR99-0018,..20,..24,..25,..26) and thirteen from California
(CA99-0014,..15,..16,..17,..20, ..21,..22,..23,..25,..26,..28,..29,..30) arrived at the testing
laboratory at temperatures that exceeded the acceptable temperature criterion. Since it
is not known what effect the elevated temperatures may have on porewater toxicity, test
results from those sediment samples were excluded from the CDF analysis. As
described in Section 2.4.2.2.2, the designation of toxicity for Arbacia bioassays utilized
two statistical test criteria for individual samples, rather than using a single survival
standard as was done with the Ampelisca bioassays. The statistical test criteria in
practice translate to a control corrected standard of approximately 85% fertilization
success or embryonic survival in the CDF based analysis of data.
99
-------
The control corrected mean percent fertilization of A. punctulata eggs in the 100% of the
water quality adjusted (WQA) porewater treatment ranged from 0.2 % to 106 %, across
the 97 stations that were included in the analysis (Figure 3.2-20). Approximately 7.4 %
of the area of the West Coast small estuaries (12 sites) had control corrected mean
percent fertilization of < 86 %, and thus would be considered to have toxic sediments
based on this bioassay. For the 50 % of WQA porewater treatment, the range of mean
percent fertilization was 5 % to 106 %, while 2.3% of estuarine area (6 sites) had values
< 86% fertilization (Figure 3.2-21). For the 25 % of WQA porewater treatment, the
range of mean percent fertilization was 50 % to 106 %, while 0.8 % of estuarine area (4
sites) had values < 85% fertilization (Figure 3.2-22).
The control corrected mean percent successful development of A. punctulata embryos
in the 100 % of WQA porewater treatment ranged from 0 % to 103 %, across the 97
stations that were included in the analysis (Figure 3.2-23). Approximately 45 % of the
area of the West Coast small estuaries (52 sites) had control corrected mean percent
embryo development success of < 87 %, and thus would be considered to have toxic
sediments based on this bioassay. For the 50 % of WQA porewater treatment, the
range of mean percent embryo development success was 0 % to 103 %, while 19.7 %
of estuarine area (27 sites) had values < 85 % embryo development success (Figure
3.2-24). For the 25 % of WQA porewater treatment, the range of mean percent embryo
development success was 0 % to 103 %, while 2.5 % of estuarine area (6 sites) had
values < 86 % embryo development success (Figure 3.2-25).
100
-------
100 -
8J
so H
so H
40 H
E
3
o
20 -
Sediment Toxicity
West Coast Small Estuaries
•Cumulative Percent
•95% Confidence Interval
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140
Percent Survival Ampelisca abdfta
Figure 3.2-19. Percent area (and 95% C.I.) of West Coast small estuaries vs. percent
control-corrected survivorship of Ampelisca abdita.
101
-------
Percent Egg Fertilization Success
of Arbacia punctulata - 100% of
Water Quality Adjusted Porewater
West Coast Small Estuaries
100 -
re
£
o>
80 -
a> 60
o>
JS 40
3
O 20
•Cumulative Percent
• 95% Confidence Interval
20 40 60 80 100
Percent Egg Fertilization Success (%)
120
Figure 3.2-20. Percent area (and 95% C.I.) of West Coast small estuaries vs. percent
fertilization at Arbacia punctulata eggs for the 100% water quality adjusted
porewater concentration.
102
-------
Percent Egg Fertilization Success
of Arbacia punctulata - 50% of
Water Quality Adjusted Porewater
West Coast Small Estuaries
100
re
£
2 80
c
o>
£
S. 60
d>
JS 40
3
E
O 20
• Cumulative Percent
• 95% Confidence Interval
20 40 60 80 100
Percent Egg Fertilization Success (%)
120
Figure 3.2-21. Percent area (and 95% C.I.) of West Coast small estuaries vs. percent
fertilization at Arbacia punctulata eggs for the 50% water quality adjusted
porewater concentration.
103
-------
Percent Egg Fertilization Success
of Arbacia punctulata - 25% of
Water Quality Adjusted Porewater
West Coast Small Estuaries
100 -
80 -
60 -
re
£
o>
o
0>
Q.
d>
.re 40
3
E
O 20
Cumulative Percent
- - - 95% Confidence Interval
—i • • " ' '•
20 40 60 80 100
Percent Egg Fertilization Success (%)
120
Figure 3.2-22. Percent area (and 95% C.I.) of West Coast small estuaries vs. percent
fertilization of Arbacia punctulata eggs for the 25% water quality adjusted
porewater concentration.
104
-------
Percent Embryonic Development Success
of Arbacia punctulata -100% of
Water Quality Adjusted Porewater
West Coast Small Estuaries
re
C
100 -
80 -
c
0)
o
S. 60
™ 40 -
3
E
u 20 H
Cumulative Percent
95% Confidence Interval
20 40 60 80 100
Percent Embryonic Development Success (%)
120
Figure 3.2-23. Percent area (and 95% C.I.) of West Coast small estuaries vs. percent
successful embryonic development of Arbacia punctulata for the 100% water
quality adjusted porewater concentration.
105
-------
Percent Embryonic Development Success
of Arbacia punctulata - 50% of
Water Quality Adjusted Porewater
West Coast Small Estuaries
100 -
80 -
60 -
re
£
o>
o
0>
Q.
d>
.re 40 -
3
E
O 20 H
0 4-i
Cumulative Percent
- - 95% Confidence Interval
20 40 60 80 100
Percent Embryonic Development Success (%)
120
Figure 3.2-24. Percent area (and 95% C.I.) of West Coast small estuaries vs. percent
successful embryonic development of Arbacia punctulata for the 50% water
quality adjusted porewater concentration.
106
-------
Percent Embryonic Development Success
of Arbacia punctulata - 25% of
Water Quality Adjusted Porewater
West Coast Small Estuaries
ra
•-
100 -
80
60
0)
£S 40
3
I
O 20
•Cumulative Percent
• 95% Confidence Interval
20 40 60 80 100
Percent Embryonic Development Success (%)
120
Figure 3.2-25. Percent area (and 95% C.I.) of West Coast small estuaries vs. percent
successful embryonic development of Arbacia punctulata for the 25% water
quality adjusted porewater concentration.
107
-------
3.2.4 Tissue Contaminants
Residues of a suite of metals, PCBs, and pesticides were measured in the whole bodies
of fish (see Table 2-5 for list of compounds). Flatfish (pleuronectiformes) were the
designated target species, while various perch-like species (perciformes) were the
secondary target group when flatfish were not captured. If neither flatfish nor perch-like
species were present, whatever abundant species was captured at the site was utilized
as an "other" group. Twelve of the fifteen sites with residues measured on the "other"
species occurred in the Northern California intensive sites. The specific fish species in
each group and their relative abundance are given in Table 3.2-3. Combined across all
three states, fish residues were measured at 145 to 152 sites, depending upon the
analyte, with flatfish measured at 112 to 119 of these sites (Tables 3.2 -4 and 3.2 -5).
Because it is not clear that the sites without any fish captured for residue analysis were
distributed randomly, and due to the uncertainties associated with mixing different guilds
of fish species, the fish residue data are presented as summary statistics rather than as
CDFs to estimate areas.
Fish tissue residues of the 11 metals measured in all three states are summarized for all
fish species combined and for each fish group in Table 3.2 -4. Aluminum, with an
average concentration of 122 ug/g for all fish species, had a residue about seven-times
greater than zinc, the metal with the second highest concentration. Silver, mercury,
cadmium, and lead had the lowest residues, with all four having a mean concentration
<0.1 ug/g when averaged for all species. The concentrations of the various metals
were generally similar among the three fish groups. The greatest difference was with
nickel, which had mean values of 0.38 ug/g and 0.11 ug/g in the flatfish and perches,
respectively, compared to an average of 2.07 ug/g in the "other" group. Though the
mean values were similar, the sample site location of the maximum tissue residues
varied for each of the metals. For example, all the mercury residues >0.05 ug/g
occurred in California, and the two residues >0.1 ug/g occurred in San Diego Bay and in
the Albion River in Northern California. In comparison, the two highest arsenic
concentrations occurred in Discovery Bay, Washington; the highest lead value occurred
in Willapa Bay, Washington; and the highest copper residues occurred in Tillamook Bay,
Oregon.
Fish tissue residues of total PCBs, total DDT, and other pesticides are summarized in
Table 3.2 -5. Total DDT had the highest residue of all the neutral organic contaminants,
averaging about 44.7 ng/g when averaged over all the fish species. 4,4'-DDE
constituted 83% to 91 % of the total DDT in all three fish groups. In contrast to the
metals, total DDT showed a considerable difference among the fish groups, ranging
from 1.92 ng/g in the "other" group to 245 ng/g in the perciform species. Total PCBs
had the second highest residue of the neutral organics, averaging about 17 ng/g for all
fish species combined. PCB138 and PCB153 were the two most abundant PCB
congeners, making up 34% to 60% of the total PCBs in the three fish groups. As with
total DDT, total PCBs showed a considerable difference among the fish groups, ranging
from about 1 ng/g in the "other" group to 83 ng/g in the perciform species. It is possible
that these differences among fish groups are largely a result of where the different types
108
-------
offish species were collected rather than an inherent difference in bioaccumulation by
the fish groups. Genyonemus lineatus (white croaker) was the most abundant species
in the perciform group, and all the white croaker used for fish residues were obtained
from either the Los Angeles Harbor or the Long Beach Harbor. These two
industrialized harbors were the sites for the maximum fish residues for both total PCBs
and total DDT and had relatively high total PCB and total DDT sediment concentrations.
In comparison, most of the individuals making up the "other" group were captured in the
non-industrialized, small, Northern California estuaries.
The residues of the thirteen additional pesticides were considerably lower than that of
total DDT (Table 3.2 -5). Endosulfan sulfate had the highest residue of the other
pesticides, with a concentration of 1.24 ng/g when averaged over all the fish species.
No other pesticide was >1 ng/g when averaged over all the fish species, though Trans-
nonachlor averaged 3.08 ng/g in the perciform species. Mirex and Toxaphene were
never detected in any fish. The three fish groups showed several differences in the
mean residues of these pesticides. None of the thirteen additional pesticides were
detected in the "other" fish group. The primary differences between the flatfish and
perch-like species were the absence of detectable levels of Endosulfan sulfate and the
higher residues of Trans-nonachlor in the perch-like species. As mentioned above,
differences in where the various species groups were collected may have contributed to
these among-group differences in residue patterns.
Tissue residues of certain organic pollutants (e.g., DDT and PCBs) and organometals
(e.g., mercury) tend to increase in larger organisms. It is not possible to directly
evaluate this effect using the EMAP data because different size fish were composited
into single analytical samples. It is possible, however, to assess whether there is any
relationship between the average size of the individuals in a composite and the
composite residue. Using mercury as the test compound, a significant positive linear
relationship was observed between average wet weight of the individuals and mercury
concentration when all fish species were combined as well as with Pleuronectes
vetulus. These preliminary results suggest that residues for the organic pollutants and
organometals would tend to be higher in larger fish in the small estuaries of the Pacific
Coast.
109
-------
Table 3.2-3. The species composition and relative abundance of the three fish groups
used in the tissue residue analysis. The percent within a group is the relative
abundance of the species within the group in which it is included. The overall percent is
the relative abundance of the species when all the fish species are combined.
Fish Group Number Percent within Overall Percent
Group
Pleuronectiformes
Pleuronectes vetulus
Platichthys stellatus
Citharichthys stigmaeus
Paralichthys californicus
Psettlchthys melanostlctus
Citharichthys sordidus
Pleuronectes isolepis
Symphurus atricauda
Perciformes
Genyonemus lineatus
Cymatogaster aggregate
Paralabrax nebulifer
Gasterosteus aculeatus
Embiotoca lateralis
Paralabrax maculatofasciatus
"Other"
Leptocottus armatus
Oligocottus rimensis
Atherinops affinis
47
43
21
10
3
1
1
1
6
5
3
2
1
1
12
2
1
37.0
33.9
16.5
7.87
2.36
0.79
0.79
0.79
33.3
27.8
16.7
11.1
5.56
5.56
80.0
13.3
6.67
29.4
26.9
13.1
6.25
1.88
0.63
0.63
0.63
3.75
3.13
1.88
1.25
0.63
0.63
7.50
1.25
0.63
110
-------
Table 3.2-4. Fish tissue residues of metals measured in all three states. The "All Fish"
group is the overall average combining all species. The species compositions of the
pleuronectiform, perciform, and "other" groups are given in Table 3.2 -3.
Metal Mean
(ug/g wet)
All Fish
Aluminum
Arsenic
Cadmium
Chromium
Copper
Lead
Mercury
Nickel
Selenium
Silver
Zinc
Pleuronectiformes
Aluminum
Arsenic
Cadmium
Chromium
Copper
Lead
Mercury
Nickel
Selenium
Silver
Zinc
Perciformes
Aluminum
Arsenic
Cadmium
Chromium
Copper
Lead
Mercury
Nickel
Selenium
Silver
Zinc
"Other"
Aluminum
Arsenic
Cadmium
122
0.60
0.03
1.11
1.25
0.06
0.02
0.52
0.37
0.01
17.7
116
0.61
0.03
1.00
1.21
0.05
0.02
0.38
0.35
0.01
18.8
117
0.76
0.01
0.46
1.30
0.10
0.05
0.11
0.52
0.01
15.06
174
0.33
0.01
SD Minimum Maximum Number
Samples
110
0.63
0.04
3.48
1.04
0.10
0.02
1.74
0.14
0.02
7.09
110
0.70
0.05
3.47
1.12
0.10
0.02
1.30
0.13
0.03
6.95
82.2
0.29
0.01
0.59
0.86
0.10
0.02
0.16
0.17
0.01
7.56
127
0.08
0.01
3.36
0.00
0.00
0.07
0.00
0.00
0.00
0.00
0.00
0.00
7.84
3.36
0
0
0.07
0
0
0
0
0
0
7.9
15.2
0.30
0.00
0.12
0.68
0.00
0.01
0.00
0.17
0.00
7.84
46.1
0.23
0.00
569
3.77
0.31
36.5
111
0.84
0.11
15.1
0.83
0.27
39.1
568
3.77
0.31
36.5
111
0.84
0.09
13.2
0.63
0.27
39.1
266
1.27
0.04
2.66
4.44
0.37
0.11
0.53
0.83
0.04
37.0
485
0.50
0.03
145
146
145
145
145
145
149
145
147
145
145
112
113
112
112
112
112
116
112
114
112
112
18
18
18
18
18
18
18
18
18
18
18
15
15
15
111
Table continued on next page
-------
Chromium
Copper
Lead
Mercury
Nickel
Selenium
Silver
Zinc
2.73
1.51
0.06
0.03
2.07
0.39
0.01
13.0
5.02
0.42
0.05
0.02
3.84
0.09
0.00
4.73
0.27
1.01
0.00
0.00
0.06
0.22
0.00
9.46
19.8
2.39
0.17
0.10
15.1
0.56
0.01
29.0
15
15
15
15
15
15
15
15
112
-------
Table 3.2-5. Fish tissue residues of total PCBs, total DDT and the additional pesticides
measured in all three states. The "All Fish" group is the overall average combining all
species. The species composition of the pleuronectiform, perciform, and "other" groups
are given in Table 3.2 -3.
Compound
All Fish
Total PCBs
Aldrin
Alpha-chlordane
Total DDT
Dieldrin
Endosulfan Sulfate
Endosulfan 1
Endosulfan II
Endrin
Heptachlor
Heptachlor Epoxide
Lindane (gamma-BHC)
Mi rex
Trans-nonachlor
Toxaphene
Pleuronectiformes
Total PCBs
Aldrin
Alpha-chlordane
Total DDT
Dieldrin
Endosulfan Sulfate
Endosulfan 1
Endosulfan II
Endrin
Heptachlor
Heptachlor Epoxide
Lindane (gamma-BHC)
Mi rex
Trans-nonachlor
Toxaphene
Perciformes
Total PCBs
Aldrin
Alpha-chlordane
Total DDT
Dieldrin
Endosulfan Sulfate
Mean
(ng/g wet)
17
0.04
0.18
44.7
0.05
1.24
0.10
0.05
0.10
0.45
0.02
0.01
0.00
0.58
0.00
8.89
0.05
0.08
19.0
0.07
1.59
0.13
0.05
0.12
0.58
0.02
0.01
0.00
0.26
0.00
83.5
0.00
0.98
245
0.00
0.00
SD Minimum Maximum Number
Samples
47.9
0.28
1.07
219
0.24
3.34
0.63
0.26
0.43
1.44
0.16
0.13
0.00
2.60
0.00
21.5
0.32
0.38
45.9
0.27
3.71
0.71
0.26
0.48
1.61
0.14
0.15
0.00
0.76
0.00
109
0.00
2.88
593
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0.00
0.00
0.00
0.00
0.00
0.00
331
2.40
11.5
2509
1.40
21.4
5.17
2.09
3.81
9.80
1.26
1.62
0.00
27.1
0.00
133
2.40
3.55
311
1.40
21.4
5.17
2.09
3.81
9.80
1.16
1.62
0.00
4.57
0.00
331
0.00
11.50
2509
0.00
0.00
152
149
149
148
149
151
150
149
149
149
149
149
149
149
149
119
116
116
115
116
118
117
116
116
116
116
116
116
116
116
18
18
18
18
18
18
113
Table continued on next page
-------
Endosulfan 1
Endosulfan II
Endrin
Heptachlor
Heptachlor Epoxide
Lindane (gamma-BHC)
Mi rex
Trans-nonachlor
Toxaphene
"Other"
Total PCBs
Aldrin
Alpha-chlordane
Total DDT
Dieldrin
Endosulfan Sulfate
Endosulfan 1
Endosulfan II
Endrin
Heptachlor
Heptachlor Epoxide
Lindane (gamma-BHC)
Mi rex
Trans-nonachlor
Toxaphene
0.00
0.08
0.06
0.00
0.07
0.00
0.00
3.08
0.00
1.08
0.00
0.00
1.92
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.36
0.24
0.00
0.30
0.00
0.00
6.87
0.00
1.89
0.00
0.00
3.22
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
1.51
1.01
0.00
1.26
0.00
0.00
27.1
0.00
4.70
0.00
0.00
9.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
18
18
18
18
18
18
18
18
18
15
15
15
15
15
15
15
15
15
15
15
15
15
15
15
114
-------
3.3 Biotic Condition Indicators
A total of 187 0.1 -m2 benthic samples (grabs or combined cores) were collected in the
three states: 47 in the base stations in California, 25 in the intensive stations in Northern
California, 49 in the base stations in Oregon, 29 in the intensive stations in Tillamook,
Oregon, and 37 in the base stations in Washington. Average penetration of the 187
samples was 10.3 cm, although five grabs and six core samples had a penetration less
than 5 cm. These eleven samples had an average benthic density about one-third
greater than the three-state average and so were included in the analysis.
3.3.1 Infaunal Species Richness and Diversity
A total of 841 benthic taxa, plus an additional 26 colonial species growing on hard
substrates (e.g., bryozoans on shell hash), were found in the 187 benthic samples. Due
to difficulties in standardizing the count of colonial species, such species were excluded
from the estimates of abundance and the count of number of species per sample.
Insects were included as a single taxon in the current analyses. Species richness
averaged 22.2 species per sample (0.1-m2) in the three states, while average species
richness among the states ranged from a low of 14.3 species per sample in Oregon to a
high of 28.6 in California (Table 3.3-1). The Northern California intensive sites tended to
have a lower species richness, and without inclusion of these sites, the species richness
increased in the base California sites to an average of 38.2 species per sample. Across
the three states, species richness ranged from 1 to 157 species per grab (0.1-m2). Of
the five benthic samples that only had one species, two occurred in California, two in
Oregon, and one in Washington. Four of these stations with low species richness
occurred at stations with bottom salinities <1 psu, while the fifth occurred at a station with
a bottom salinity of 13.9 psu. Of the three stations with >100 species per sample, two
occurred in Discovery Bay and the other in Freshwater Bay, both in the Strait of Juan de
Fuca, Washington. All these stations with high species richness had bottom salinities
>30 psu.
On an areal basis, approximately 50% of the area of the West Coast small estuaries had
a species richness of < 17 species per sample, and 90% of the area had a species
richness less than 62 species per sample (Figure 3.3-1). Because of the small area of
the Northern California estuaries compared to rest of the coast, exclusion of the Northern
California intensive sites had an inconsequential effect on these areal estimates.
The diversity index H' (log base 2 derived) averaged 2.33 in the three states and ranged
from 0 to 5.93 (Table 3.3-1). Across the states, average H' ranged from a low of 1.88 in
Oregon to a high of 2.68 in California. H' tended to be lower in small Northern California
estuaries, and for comparison, the exclusion of these intensive sites increased the
average for the California base station to 3.33. The stations with an H' of 0 were the five
stations with a single species per sample mentioned above. The maximum H' (5.93)
occurred in the Discovery Bay, Washington, sample that contained 147 species.
115
-------
On an areal basis, 50% of the area of the West Coast small estuaries had an H' less
than 2.80, and 90% of the area had an H' less than 4.18 (Figure 3.2 -2). As with
species richness, exclusion of the Northern California stations had almost no effect on
these areal estimates.
3.3.2 Infaunal Abundance and Taxonomic Composition
Benthic density averaged 1378.9 individuals per sample in the three states and ranged
from 1 to 41,582 individuals per sample (Table 3.3-1). Average density across the
states ranged from a low of 482.5 individuals per sample in Washington to a high of
2620.7 individuals per sample in California (Table 3.3-1). Benthic density in the
Northern California intensive sites tended to be higher than the rest of the state, and if
these small estuarine systems are excluded, benthic density averaged 1033.0
individuals per sample in the base stations in California (Table 3.3-1). Across the three
states, six stations had densities <10 individuals/sample. Three of these low-density
stations occurred at sites with a salinity <0.5 psu, while the other three occurred at sites
with salinities ranging from about 1 to 9 psu. The two stations with the greatest benthic
densities, 41,582 and 32,285 individuals per sample, both occurred in the Smith River in
Northern California. The only other station with >20,000 individuals/sample occurred in
the Little River, also in Northern California. The amphipods Americorophium spinicorne
and A. salmonis constituted between 89% and 98% of the individuals at these stations.
Salinity at these Smith River stations was 8-10 psu, while salinity at the Little River
station was 31.2 psu.
On an areal basis, 50% of the area of the West Coast small estuaries had a benthic
density less than 151 individuals/sample, and 90% of the area had a density less than
1157 individuals/sample (Figure 3.3-3). As with species richness and H' diversity,
exclusion of the Northern California stations had an inconsequential effect on the these
areal estimates.
The abundance, taxonomic grouping, and classification of the 10 most abundant benthic
species from the three states are given in Table 3.3-2. These ten numerically dominant
species made up 75% of the total fauna. The amphipods Americorophium spinicorne
and A. salmonis were the two most abundant species, making up 54% of the total
fauna. Oligochaetes were the third most abundant taxon, making up 7% of the total
fauna, as well as being the most frequently captured taxon. Of the remaining seven
numerically abundant species, six were polychaetes and one was an amphipod. The
maximum abundances of six of the numerically dominant species, including all three
amphipod species, occurred in the small estuaries of Northern California. With their
high densities and small area, the Northern California intensive sites have a
disproportionate impact on the three-state summary statistics. Therefore, the summary
statistics for the three states are also presented for the 10 most abundant benthic
species excluding the Northern California intensive sites (Table 3.3-3). Americorophium
spinicorne and A. salmonis were still the two most abundant species in the three states,
although their densities were only about 15% to 30% of their values when Northern
California was included. Another difference when the Northern California stations are
excluded is that the polychaete Owenia fusiformis and the amphipod Grandidierella
japonica were included among the numerically dominant species while Neanthes and
Eogammarus drop out.
Tables 3.3-2 and 3.3-3 list the classification of the numerically dominant species as
native, nonindigenous, cryptogenic, or indeterminate. Cryptogenic species are species
of uncertain geographic origin (Carlton, 1996), while indeterminate taxa are those taxa
not identified to a sufficiently low level to classify as native, nonindigenous, or
116
-------
cryptogenic (Lee et al., 2003). Of the 10 numerically dominant species (Table 3.3-2),
five were native, two were indeterminate, two were nonindigenous, and one was
classified as cryptogenic. These three nonindigenous and cryptogenic species
constituted less than 6% of the total benthic abundance. When the Northern California
sites are excluded, the ten numerically dominant species in the three states are
composed of three natives, two indeterminate taxa, three nonindigenous species, and
two cryptogenic species (Table 3.3-3). The relative abundance of the combined,
numerically dominant nonindigenous and cryptogenic species was 15.3% (Table 3.3-3)
when the Northern California sites were excluded. This contribution to total abundance
was more than twice the relative abundance (5.7%, Table 3.3-2) calculated when the
Northern California sites were included.
117
-------
Benthic Species Richness
West Coast Small Estuaries
100
so-i
c
0)
0)
40
E
3
o
20-
- - . . .95% Confidence Interval
20 40 60 80 100
Number of Species
120
140
160
Figure 3.3-1. Percent area (and 95% C.I.) of West Coast small estuaries vs. benthic
infaunal species richness.
118
-------
Shannon-Weiner Diversity Index
West Coast Small Estuaries
100
re
80
0)
5 60
Q.
0)
o
20
- - - - .95% Confidence Interval
H1
Figure 3.3-2. Percent area (and 95% C.I.) of West Coast small estuaries vs. benthic
infaunal H' diversity.
119
-------
Total Number of Benthic Organisms
West Coast Small Estuaries
Cumulative Percent
- - - - .95% Confidence Interval
5000 10000
15000 20000 25000 30000
Number of Organisms
35000 40000 45000
Figure 3.3-3. Percent area (and 95% C.I.) of West Coast small estuaries vs. benthic
infaunal total abundance.
120
-------
Table 3.3-1. Summary statistics for benthic abundance, number of species per benthic sample, and H'. All values are
calculated per 0.1 m2 benthic sample. The 3-State values include the base and intensive stations from California, Oregon
and Washington (N=187). The California values are calculated both for the base stations with the intensive stations in
Northern California included (N=72), and for the base stations without the California intensive sites (N=47). The Oregon
values are calculated for the base stations with the intensive stations in Tillamook Bay (N=78). The Washington values
are calculated for the base stations (N=37).
Location Parameter
3-State: Individuals/sample
3-State: Spp/sample
3-State: H'
CA: Individuals/sample
CA: Spp/sample
CA: H'
CA base wo/N. CA: Individuals/sample
CA base wo/N. CA: Spp/sample
CA base wo/N. CA: H'
OR: Individuals/sample
OR: Spp/sample
OR: H'
WA: Individuals/sample
WA: Spp/sample
WA: H'
Mean
1378.9
22.2
2.33
2620.7
28.6
2.68
1033.0
38.2
3.33
657.7
14.3
1.88
482.5
26.5
2.58
SD
4264.8
23.5
1.26
6580.3
23.7
1.35
1442.3
23.6
1.13
1191.4
11.6
0.96
710.1
34.9
1.37
Min
3
1
0
7
1
0
12
5
1.34
7
1
0
3
1
0
Max
41,582
147
5.93
41,582
95
5.24
7383
95
5.24
8118
65
4.10
3106
147
5.93
-------
Table 3.3-2. Abundance, taxonomic grouping, and classification of the ten most abundant benthic species in the three
states including the intensification sites in Northern California and Tillamook, Oregon (N=187). * = maximum value
occurred in the Northern California intensification sites. Taxonomic groupings: A = amphipod, 0 = oligochaete, P =
polychaete. Classification of the species: Native, NIS = nonindigenous, Crypto. = cryptogenic, Indeter. = indeterminate
taxa (see text for definitions).
Americorophium spinicorne
Americorophium salmonis
Oligochaeta
Eogammarus confervicolus
Complex
Streblospio benedicti
Mediomastus sp
Mediomastus californiensis
Pygospio elegans
Pseudopolydora
paucibranchiata
Neanthes limnicola
Taxon
A
A
O
A
P
P
P
P
P
P
Class
Native
Native
Indeter.
Native
NIS
Indeter.
Native
Crypto.
NIS
Native
Mean
524.2
220.9
96.7
35.4
29.2
28.0
26.4
25.9
23.4
19.7
SD
3389.8
1257.7
343.1
198.5
189.8
86.3
120.9
202.5
216.3
94.7
Max
39,700*
14,728*
3,219*
1953*
1889
668
1162
1963
2772
1004*
Min
0
0
0
0
0
0
0
0
0
0
Percent
Abundance
38.0
16.0
7.0
2.6
2.1
2.0
1.9
1.9
1.7
1.4
Percent
Frequency
27.8
34.8
56.7
19.8
13.9
39.6
22.5
14.4
16.0
29.4
-------
Table 3.3-3. Abundance, taxonomic grouping, and classification of the ten most abundant benthic species in the three
states excluding the Northern California intensification stations (N=162). Taxonomic groupings: A = amphipod, 0 =
oligochaete, P = polychaete. Classification of the species: Native, NIS = nonindigenous, Crypto. = cryptogenic, Indeter.
indeterminate taxa (see text for definitions).
Americorophium spinicorne
Americorophium salmonis
Oligochaeta
Mediomastus sp
Mediomastus californiensis
Pygospio elegans
Pseudopolydora
paucibranchiata
Streblospio benedicti
Owenia fusiformis
Grandidierella japonica
Taxon
A
A
O
P
P
P
P
P
P
A
Class
Native
Native
Indeter.
Indeter.
Native
Crytpo.
NIS
NIS
Crypto.
NIS
Mean
77.4
67.8
59.1
32.3
30.5
29.6
26.9
25.2
16.0
13.2
SD
515.5
261.8
232.9
92.0
129.5
217.4
232.2
174.2
154.7
69.3
Max
6147
2598
2393
668
1162
1963
2772
1889
1890
637
Min
0
0
0
0
0
0
0
0
0
0
Percent
Abundance
10.7
9.3
8.1
4.4
4.2
4.1
3.7
3.5
2.2
1.82
Percent
Frequency
19.8
34.0
53.1
45.1
24.7
13.6
16.7
14.8
9.3
24.7
CO
-------
3.3.3 Demersal Species Richness and Abundance
To measure abundance and composition, fish were sampled with 16-foot bottom otter
trawls in all three states. There was a total of 144 successful trawls of at least 5 minute
duration across the three states, with 37 in the base stations in California, 2 in the
intensive stations in Northern California, 43 in the base stations in Oregon, 28 in the
intensive stations in Tillamook, Oregon, and 34 in Washington. Trawls were pulled at
an average speed of 1.7 knots for an average duration of 9.9 minutes (Table 3.3-4).
Due to the number of stations without successful trawls, the analysis of the fish trawl
data is limited to summary statistics and species composition, and no CDFs are
presented.
Table 3.3-5 shows the mean number of individuals and species captured per trawl for
the three states combined and in each of the individual states. The number of
individuals per trawl averaged 33.7 fish per trawl, with a low of 13.9 in Oregon and a
high of 68.0 in California. Species richness averaged 3.53 fish species per trawl, with a
|ow of 2.63 in Oregon and a high of 5.46 in California. A total of 77 fish species were
identified from the base stations in the three states, and no additional fish species were
collected from the additional trawls in the small Northern California estuaries and
Tillamook Bay. However, two additional species, Oligocottus maculosus and Salmo
clarkii, were captured in beach seines at a station in Washington that was too shallow to
pull the otter trawl. The results from these seines are not included in the summary
statistics.
The 10 most abundant fish species across the entire coast are given in Table 3.3-6.
These 10 numerically dominant species constituted 81% of the total fauna.
Pleuronectes vetulus, the English sole, was both the most abundant and frequently
collected species along the West Coast. Citharichthys stigmaeus, the speckled
sanddab, was the second most abundant fish. These two flatfish made up more than
50% of the individuals captured in the three states and were among the top five most
abundant species in all three states (Table 3.3-7). Oregon and Washington had similar
species composition and shared four of the five numerically dominant species (Table
3.3-7). Two of the abundant species in California, Genyonemus lineatus and Seriphus
politus, were not found in the other states.
124
-------
Table 3.3-4. Trawl duration and speed averaged across California, Oregon, and Washington (N=141) and in each
individual state. SD = standard deviation. Durations are given in minutes and fractions of minutes. Trawls with durations
less than 5 minutes were not use in the analysis and are not included in the table.
Location: Parameter
3-State: Trawl duration (Min.)
3-State: Trawl speed (Knots)
CA: Trawl duration (Min.)
CA: Trawl speed (Knots)
OR: Trawl duration (Min.)
OR: Trawl speed (Knots)
WA: Trawl duration (Min.)
WA: Trawl speed (Knots)
Mean
9.9
1.7
9.8
2.0
9.8
1.6
10.0
1.3
SD
1.18
0.41
1.06
0.27
1.25
0.39
1.20
0.17
Maximum
15.0
3.1
12.0
3.1
13.0
2.4
15.0
1.6
Minimum
5.0
0.9
5.0
1.0
5.0
0.9
7.0
1.0
Oi
-------
Table 3.3-5. Mean number of fish captured per trawl and mean number of fish species per trawl averaged across
California, Oregon, and Washington (N=144) and for each individual state. SD = standard deviation.
Location: Parameter
3-State: Individuals/trawl
3-State: Species/trawl
CA: Individuals/trawl
CA: Species/trawl
OR: Individuals/trawl
OR: Species/trawl
WA: Individuals/trawl
WA: Species/trawl
Mean
33.7
3.53
68.0
5.46
13.9
2.63
35.5
3.18
SD
72.9
2.68
111.0
3.77
18.2
1.38
76.6
2.10
Minimum
0
0
0
0
1
1
1
1
Maximum
496
17
496
17
111
6
336
10
Percent
Frequency
(%)
99.3
99.3
97.4
97.4
100
100
100
100
O)
-------
Table 3.3-6. Ten numerically dominant fish species averaged across California, Oregon, and Washington, including both
the base and intensive stations (N=144). Relative abundance is the percentage the species makes up of the total
abundance. Frequency is the number (or percent) of trawls in which each species was captured in the three states.
Scientific Name
Pleuronectes vetulus
Citharichthys stigmaeus
Cymatogaster aggregata
Platichthys stellatus
Genyonemus lineatus
Microgadus proximus
Ophiodon elongatus
Spirinchus thaleichthys
Leptocottus armatus
Seriphus politus
Common Name
English sole
Speckled sanddab
Shiner perch
Starry flounder
White croaker
Pacific tomcod
Lingcod
Longfin smelt
Pacific staghorn
sculpin
Queenfish
Mean
Individuals/
Trawl
10.40
6.75
2.83
1.98
1.07
0.90
0.89
0.88
0.88
0.83
SD
Individuals/
Trawl
34.63
23.96
17.08
4.90
7.71
8.72
4.66
7.55
2.22
8.24
Max
Individuals/
Trawl
256
194
193
33
76
104
40
79
13
97
Relative
Abundance
(%)
30.9
20.0
8.4
5.9
3.2
2.7
2.6
2.6
2.6
2.4
Frequency
(% Frequency)
67
(46.5%)
46
(31 .9%)
35
(24.3%)
53
(36.8%)
9
(6.3%)
7
(4.9%)
13
(9.0%)
4
(2.8%)
41
(28.5%)
3
(2.1%)
-------
Table 3.3-7. Mean and standard deviation of the five most numerically abundant fish species in California, Oregon, and
Washington. The California and Oregon values include both the base and intensive stations. Frequency is the number
(or percent) of trawls in which each species was captured within the state. N = 39 in California; N = 71 in Oregon; N = 34
in Washington.
California
Species
Citharichthys
stigmaeus
Pleuronectes
vetulus
Genyonemus
lineatus
Ophiodon
elongatus
Seriphus
politus
California
Mean/Trawl
(SD)
19.3
(42.1)
16.9
(47.9)
3.9
(14.6)
3.1
(8.6)
3.1
(15.8)
California
Frequency
17
(43.6%)
11
(28.2%)
9
(23.1%)
9
(23.1%)
3
(7.7%)
Oregon
Species
Pleuronectes
vetulus
Platichthys
stellatus
Cymatogaster
aggregate
Microgadus
proximus
Citharichthys
stigmaeus
Oregon
Mean/Trawl
(SD)
3.9
(6.6)
2.7
(5.1)
1.7
(4.9)
1.6
(12.4)
1.3
(3.7)
Oregon
Frequency
38
(53.5%)
37
(52.1%)
22
(31 .0%)
2
(2.8%)
17
(23.9%)
Washington
Species
Pleuronectes
vetulus
Cymatogaster
aggregate
Citharichthys
stigmaeus
Platichthys
stellatus
Spirinchus
thaleichthys
Washington
Mean/Trawl
(SD)
16.6
(47.8)
6.4
(33.0)
3.8
(12.5)
2.6
(6.6)
1.3
(7.7)
Washington
Frequency
18
(52.3%)
7
(21 .3%)
12
(35.3%)
13
(38.2%)
1
(2.9%)
00
-------
4.0 References
American Society for Testing and Materials (ASTM). 1991. Guide for conducting 10-day
static sediment toxicity tests with marine and estuarine amphipods. ASTM
Standard Methods Volume 11.04, Method Number E-1367-90. ASTM,
Philadelphia, PA.
Bourgeois, P.E., V.J. Sclafani, J.K. Summers, S. C. Robb, and B.A.Vairin. 1998. Think
before you sample. GEOWorld. Vol. 11: No 12.
Carlton, J. T. 1996. Biological invasions and cryptogenic species. Ecology 77:1653-1654.
Carlton, J.T. and J.B. Geller. 1993. Ecological roulette: the global transport of
nonindigenous marine organisms. Science 261: 78-82.
Cohen, A. and Carlton, J.T. 1995. Nonindigenous aquatic species in a United States
estuary: A case study of the biological invasions of the San Francisco Bay and
Delta. Report for the National Sea Grant College Program, DT and the U.S. Fish
and Wildlife Service, Washington, D.C. Report No. PB 96-166525.
Cooper, S.R. and G.S. Brush. 1991. Long-term history of Chesapeake Bay anoxia.
Science 254:993-996.
Cooper, L. 2000. West EMAP Revised Information Management Plan for 2000. Draft. 14
p. plus Appendices A-D.
Copping, A. and B.C. Bryant. 1993. Pacific Northwest Regional Marine Research
Program, Vol. 1. Research Plan, 1992-1996. Office of Marine Environmental and
Resource Programs, University of Washington, Seattle.
Culliton, T.J., M.A. Warren, T.R. Goodspeed, D.G. Remeer, C.M. Blackwell, and
J.J. McDonough, III. 1990. 50 Years of Population Change along the Nation's
Coasts, 1960-2010. NOAA, Office of Oceanography and Marine Assessment,
National Ocean Service, Coastal Trends Series, Rockville, MD. pp 41.
Diaz-Ramos, S., D.L. Stevens, Jr., and A.R. Olsen. 1996. EMAP Statistics Methods
Manual. EPA/620/R-96/002. Corvallis, OR: U.S. Environmental Protection
Agency, Office of Research and Development, National Health and Environmental
Effects Research Laboratory.
Durning, AT. 1996. The six floods. WorldWatch November/December 1996. pp. 28-36.
Geider, R. J. and J. La Roche. 2002. Redfield revisited: variability of C:N:P in marine
microalgae and its biochemical basis. European Journal Phycology 37: 1-17.
Holland, A.F. and AT. Shaughnessey. 1986. Separation of long term variation in benthic
organisms into major components. In: Oceans 86 Conference Record. Vol. 3.
Monitoring strategies symposium. Institute of Electrical and Electronic Engineers,
Piscataway, NJ. pp. 1056-1061.
Howarth, R.W. J.R. Fruch and D. Sherman. 1991. Inputs of sediment and carbon to an
estuarine ecosystem: influence of land use. Ecological Applications 1:27-39.
129
-------
Hyland, J.L., L. Balthis, C.T. Hackney, G. McRae, A.M. Ringwood, T.R. Snoots, R.F.
Van Dolah, and T.L. Wade. 1998. Environmental quality of estuaries of the
Carolinian Province: 1995. Annual statistical summary for the 1995 EMAP-
Estuaries Demonstration Project in the Carolinian Province. NOAA Technical
Memorandum NOS ORCA 123 NOAA/NOS, Office of Ocean Resources
Conservation and Assessment, Silver Spring, MD. 143 p.
Hyland, J.L., T.J. Herrlinger, T.R. Snoots, A.M. Ring-wood, R.F. Van Dolah, C.T.
Hackney, G.A. Nelson, J.S. Rosen, and S.A. Kokkinakis. 1996. Environmental
Quality of Estuaries of the Carolinian Province: 1994. Annual Statistical Summary
for the 1994 EMAP- Estuaries Demonstration Project in the Carolinian Province.
NOAA Technical Memorandum NOS ORCA 97. NOAA/NOS, Office of Ocean
Resources Conservation and Assessment, Silver Spring, MD. 102 p.
Lauenstein, G. G. and A. Y. Cantillo (eds.). 1993. Sampling and analytical methods of
the National Status and Trends Program National Benthic Surveillance and
Mussel Watch Projects 1984-1992: Comprehensive descriptions of trace organic
analytical methods, Volume IV NOAA Technical Memorandum NOS ORCA 71,
Silver Spring, MD. 182 pp.
Lauenstein, G.G., Crecelius, E.A. and Cantillo, A.Y. 2000. Baseline metal
concentrations of the U.S. West Coast and their use in evaluating sediment
contamination. Presented at 21st Ann. Soc. Environ. Toxicology and Chemistry
meeting, November 12-15, 2000, Nashville Tennessee.
Lee, H.ll, B. Thompson, and S. Lowe. 2003. Estuarine and scalar patterns of invasion in
the soft-bottom benthic communities of the San Francisco estuary. Biological
Invasions 5:85-102.
Leppakoski, E. 1979. The use of zoobenthos in evaluating effects of pollution in
brackish-water environments. In: The use of ecological variables in
environmental monitoring. The National Swedish Environment Protection Board,
Report PM 1151. pp. 151-157.
Long, E.R., D.D. MacDonald, S.L. Smith, and F.D. Callander. 1995. Incidence of
adverse biological effects within ranges of chemical concentrations in marine and
estuarine sediments. Environmental Management 19:81-97.
Long, E.R., Hameedi, J., Robertson, A., Dutch, M., Aasen, S., Welch, K., Magoon, S.,
Carr, R., Johnson, T., Biedenbach, J., Scott, K., Mueller, C., and Anderson, J.
2000. Sediment Quality in Puget Sound. Year 2 - Central Puget Sound. National
Oceanic and Atmospheric Administration, National Ocean Service, Silver Spring,
MD. NOS NCCOS CCMA Technical Memo No. 147 , and Washington State
Department of Ecology, Olympia, WA, Publication No. 00-03-055. pp. 353.
Macauley, J.M., J.K. Summers, P.T. Heitmuller, V.D. Engle, G.T. Brooks, M. Babikow,
and A.M. Adams. 1994. Annual Statistical Summary: EMAP - Estuaries Louisiana
Province -1992. U.S. EPA Office of Research and Development, Environmental
Research Laboratory, Gulf Breeze, FL. EPA/620/R-94/002. 82 p. plus Appendix A.
130
-------
Macauley, J.M., J.K. Summers, V.D. Engle, P.T. Heitmuller, and A.M. Adams. 1995.
Annual Statistical Summary: EMAP - Estuaries Louisiana Province -1993. U.S.
EPA Office of Research and Development, Environmental Research Laboratory,
Gulf Breeze, FL. EPA/620/R-96/003. 95 p.
Reish, D.J. 1986. Benthic invertebrates as indicators of marine pollution: 35 years of
study. In: Oceans 86 Conference Record. Vol. 3. Monitoring strategies
symposium. Institute of Electrical and Electronic Engineers, Piscataway, NJ pp.
885-888.
Simenstad, C.A., J.A. Estes, and K.W. Kenyon. 1978. Aleuts, sea otters, and alternate
stable state communities. Science 200:403-411
Simenstad, C.A. and R. Thorn. 1995. Spartina alterniflora (smooth cordgrass) as an
invasive halophyte in Pacific Northwest estuaries. Hortus Northwest 6:9-12, 38-39.
Stevens, D.L. Jr. 1997. Variable density grid-based sampling designs for continuous
spatial populations. Environmetrics 8:167-195.
Stevens, D. I., Jr. and A.R. Olsen. 1999. Spatially restricted surveys over time for
aquatic resources. J. of Agricultural, Biological and Environmental Statistics:
4:415-428.
Strobel, C.J., H.W. Buffum, S.J. Benyi, E.A. Petrocelli, D.R. Reifsteck, and D.J. Keith.
1995. Statistical summary: EMAP - Estuaries Virginian Province -1990 to 1993.
U.S. EPA National Health and Environmental Effects Research Laboratory, Atlantic
Ecology Division, Narragansett, R.I. EPA/620/R-94/026. 72 p. plus Appendices
A-C.
Strobel, C.J., S.J. Benyi, D.J. Keith, H.W. Buffum, and E.A. Petrocelli. 1994. Statistical
summary: EMAP -Estuaries Virginian Province -1992. U.S. EPA Office of
Research and Development, Environmental Research Laboratory, Narragansett,
Rl. EPA/620/R-94/019. 63 p. plus Appendices A-C.
Summers, J.K., J.M. Macauley, P.T. Heitmuller, V.D. Engle, A.M. Adams, and G.T.
Brooks. 1993. Annual Statistical Summary: EMAP-Estuaries Louisianian Province -
1991. U.S. Environmental Protection Agency, Office of Research and
Development, Environmental Research Laboratory, Gulf Breeze, FL. EPA/620/R-
93/007. p. plus Appendices A-C.
Taylor, J. 1987. Quality assurance of chemical measurements. Lewis Publishers, Inc,
Chelsea, Ml.
T N & Associates, Inc. 2001. Compiling Lists of Nonindigenous Species (NIS) from the
West Coast of the Unites States, Excjuding San Francisco Bay. Final Report
submitted to: National Center for Environmental Assessment - Washington Office,
U.S. Environmental Protection Agency, Washington, D.C. Contract No. 68-C-98-
187. 11 p. plus Appendices, plus Spreadsheet.
U.S. EPA. 1994a. Methods for Assessing the Toxicity of Sediment-associated
Contaminants with Estuarine and Marine Amphipods. Office of Research and
Development, Environmental Monitoring and Systems Laboratory, Cincinnati, OH.
EPA 600-R-94-025. June 1994.
131
-------
U.S. EPA. 1994b. Environmental Monitoring and Assessment Program (EMAP):
Laboratory Methods Manual - Estuaries, Volume 1: Biological and Physical
Analyses. Office of Research and Development, Environmental Monitoring and
Systems Laboratory, Cincinnati, OH. EPA/600/4-91/024. 321-324.
U.S. EPA. 2000. Clean Water Action Plan: National Coastal Condition Report. United
States Environmental Protection Agency, Office of Research and Development/
Office of Water. Washington D.C. EPA620-R-00-004
U.S. EPA. 2001 a. Environmental Monitoring and Assessment Program (EMAP):
National Coastal Assessment Quality Assurance Project Plan 2001-2004. United
States Environmental Protection Agency, Office of Research and Development,
National Health and Environmental Effects Research Laboratory, Gulf Ecology
Division, Gulf Breeze, FL. EPA/620/R-01/002.
U.S. EPA. 2001 b. National Coastal Assessment: Field Operations Manual.
EPA/620/R-01/003. 71 pp.
U.S. EPA. 2004. National Coastal Condition Report II. EPA/620/R-03/002. In press.
U.S. General Accounting Office (GAO). 2000. Water Quality - EPA and State Decisions
Limited by Inconsistent and Incomplete Data. Report to the Chairman,
Subcommittee on Water Resources and Environment, Committee on
Transportation and Infrastructure, House of Representatives. Report GAO/RCED
00-54. 78pp.
U.S. Geological Survey (USGS). 2000. Toxicity testing of sediments from the
BEST/EMAP Western Estuary Group monitoring study. Report Submitted by the
USGS Columbia Environmental Research Center, Marine Ecotoxicology
Research Station to the U.S. Geological Survey. Biomonitoring and
Environmental Status and Trends Program, 6006 Schroeder Road, Madison, Wl,
10 pp. + 22 tables, 3 figures and 4 attachments.
U.S. Geological Survey (USGS). 2001. H4IIE bioassay-derived 2,3,7,8 -
tetrachlorodibenzo-p-dioxin equivalents (TCDD-EQ) in fish collected in 1999 from
small estuaries along the western coast of the United States. Report Submitted
by the USGS Columbia Environmental Research Center to the U.S. Geological
Survey. Biomonitoring and Environmental Status and Trends Program, 6006
Schroeder Road, Madison, Wl, 16 pp. + 8 figures, 10 tables.
Weisberg, S.B., J.B. Frithsen, A.F. Holland, J.F. Paul, K.J. Scott, J.K. Summers, H.T.
Wilson, R. Valente, D.G. Heimbuch, J. Gerritsen, S.C. Schimmel, and R.W.
Latimer. 1992. EMAP- Estuaries Virginian Province 1990 demonstration project
report. U.S. EPA Environmental Research Laboratory, Narragansett, R.I.
EPA/600/R-92/100.
132
-------
-------
United States
Environmental Protection
Agency
Please mate all necessary changes on the below label,
detach or copy, and return to the addrass in the upper
left-hand corner
If you do not wish to receive these reports CHECK HERE [J;
detach, or copy this cover, and retyrn to the address in the
upper left-hand corner.
PRESORTED STANDARD
POSTAGE & FEES PAID
EPA
PERMIT No. G-35
Research and Development (8101R)
Washington, DC 20460
Official Business
Penalty for Private Use
$300
EPA Report 620/R-04/200
February 2005
www.epa.gov
Recycled/Recyclable
Printed with vepetable-based ink on
that contains & minimum of
S0% post-eoosunier fttoeT content
processed eMori>n« frs©
------- |