United States
Environmental Protection
Agency

        n of Estuaries
          I
      A Statistical Summary
 ARCH  AND
LOP

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                                          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

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                                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

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                                   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.

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                              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

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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

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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

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                          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

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            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



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            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

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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

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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
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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

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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

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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

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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

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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.

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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

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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

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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.

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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

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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:

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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.

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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

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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

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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.

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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

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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.

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  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

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                          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

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           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

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                   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

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        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

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  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

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                                            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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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.
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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

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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)
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      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

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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

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     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

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     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.

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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

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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

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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

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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

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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

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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)

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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

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    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

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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

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 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

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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

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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

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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

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54

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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

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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

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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

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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

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         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

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                        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

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                  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

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                    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

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                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

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               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

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                                  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

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                          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

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                        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

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                                 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

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                                         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

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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

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                           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

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                            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

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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

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                        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

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                          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

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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

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                       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

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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

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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

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            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

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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

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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

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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

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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

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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

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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

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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

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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

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                           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

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                       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

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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

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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

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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)

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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

-------
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      Chelsea, Ml.

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      U.S. Environmental Protection Agency, Washington, D.C. Contract No. 68-C-98-
      187. 11  p. plus Appendices, plus Spreadsheet.

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U.S. EPA. 1994b. Environmental Monitoring and Assessment Program (EMAP):
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      Office of Water. Washington D.C. EPA620-R-00-004

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      tetrachlorodibenzo-p-dioxin equivalents (TCDD-EQ) in  fish collected in 1999 from
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