**NEAR FIELD RECEIVING WATER MONITORING OF TRACE METALS IN CLAMS
(*MACOMA BALTHICA*) AND SEDIMENTS NEAR THE PALO ALTO WATER QUALITY
CONTROL PLANT IN SOUTH SAN FRANCISCO BAY, CALIFORNIA: 1999-2001**

\_**\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_**

**U. S. GEOLOGICAL SURVEY**

**OPEN FILE REPORT 02-453**

Prepared in cooperation with the

**CITY OF PALO ALTO, CALIFORNIA**

**NEAR FIELD RECEIVING WATER MONITORING OF TRACE METALS IN CLAMS
(*MACOMA BALTHICA*) AND SEDIMENTS NEAR THE PALO ALTO WATER QUALITY
CONTROL PLANT IN SOUTH SAN FRANCISCO BAY, CALIFORNIA: 1999-2001**

Carlos Primo C. David, Samuel N. Luoma, Cynthia L. Brown, Daniel J.
Cain, Michelle I. Hornberger

and Irene R. Lavigne

\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_

U. S. GEOLOGICAL SURVEY

OPEN FILE REPORT 02-453

Prepared in cooperation with the

CITY OF PALO ALTO, CALIFORNIA

Menlo Park, California

U. S. DEPARTMENT OF THE INTERIOR

GAIL NORTON, Secretary

U. S. GEOLOGICAL SURVEY

CHARLES GROAT, Director

For additional information Copies of this report may be

write to: obtained from the authors or

Samuel N. Luoma, MS 465 U. S. Geological Survey

U.S. Geological Survey Information Center

345 Middlefield Road Box 25286, MS 517

Menlo Park, CA 94025 Denver Federal Center

Denver, CO 80225

**CONTENTS**

\_\_\_\_\_\_\_\_

Page

Abstract .. 1

Introduction 2

Purpose 2

Study Site 3

Methods 3

Results and Discussion 5

References Cited 8

Appendix 1: Palo Alto Sediments 45

Appendix 2: Palo Alto Clams 63

**ILLUSTRATIONS**

\_\_\_\_\_\_\_

Figure 1. Map showing sampling station at Palo Alto in South San
Francisco Bay 10

> 2\. Graph showing water column salinity from 1994 through 2001 at Palo
> Alto 11
>
> 3\. Graph showing percent silt/clay, iron and aluminum in sediments at
> Palo Alto from 1994 through 2001 12
>
> 4\. Graph showing concentrations of chromium, vanadium and nickel in
> sediments in 1994 through 2001 at Palo Alto 13
>
> 5\. Graph showing near-total and acid-extractable copper
> concentrations in sediments from 1994 through 2001 at Palo Alto 14
>
> 6\. Graph showing near-total and acid-extractable zinc concentrations
> in sediments from 1994 through 2001 at Palo Alto 15
>
> 7\. Graph showing acid-extractable silver concentrations in sediments
> from 1990 through 2001 at Palo Alto 16
>
> 8\. Graph showing concentrations of cadmium in sediments from 1994
> through 1999 at Palo Alto 17
>
> 9\. Graph showing concentrations of selenium and mercury in sediments
> from 1994 through 2001 at Palo Alto 18
>
> 10\. Graph showing annual mean concentrations of copper in the clam
> *Macoma balthica* from 1977 through 2001 at Palo Alto 19
>
> 11\. Graph showing annual mean concentrations of silver in the clam
> *Macoma balthica* from 1977 through 2001 at Palo Alto 20
>
> 12\. Graph showing concentrations of copper in clams (*Macoma
> balthica*) at Palo Alto from 1994 through 21
>
> 13\. Graph showing concentrations of silver in clams (*Macoma
> balthica*) at Palo Alto from 1994 through 22
>
> 14\. Graph showing concentrations of zinc in clams (*Macoma balthica*)
> at Palo Alto from 1994 through 2001 23
>
> 15\. Graph showing concentrations of chromium in clams (*Macoma
> balthica*) at Palo Alto from 1994 through 2001 24
>
> 16\. Graph showing concentrations of nickel in clams (*Macoma
> balthica*) at Palo Alto from 1994 through 25
>
> 17\. Graph showing selenium in sediments and clams from 1994 through
> 2001 at Palo Alto 26
>
> 18\. Graph showing concentrations of mercury in clams (*Macoma
> balthica*) at Palo Alto from 1994 through 2001 27
>
> 19\. Graph showing the weight of *Macoma balthica* of 25mm shell
> length (condition index)
>
> as determined between 1988 through 2001 at Palo Alto 28
>
> 20\. Correlation of maximum condition index in *Macoma balthica* vs.
> maximum copper
>
> concentrations in the months preceding the determination of maximum
> condition 29

**TABLES**

\_\_\_\_\_\_

Table 1. Trace element concentrations in standard reference material
from San Joaquin soils

(NIST 2709) for 2000 and
2001.................................................................................30

2\. Trace element concentrations in standard reference material from
bovine liver tissue (NRCC TORT2) and from lobster hepatopancreas tissues
(NIST 2976) 32

> 3\. Sediment and environmental characteristics at Palo Alto in 1999,
> 2000, and 2001 34
>
> 4\. Trace element concentrations in sediments at Palo Alto in 1999,
> 2000, and 2001 37

5.  Trace element concentrations in clams (*Macoma balthica*) from Palo
    Alto

> in 1999, 2000, and 2001 40

6\. Annual mean copper concentrations in clams and sediments: 1977 to
2001 43

> 7\. Annual mean silver concentrations in clams and sediments from Palo
> Alto

Mudflat: 1977‑2001 44

NEAR FIELD RECEIVING WATER MONITORING OF TRACE METALS IN CLAMS (*MACOMA
BALTHICA*) AND SEDIMENTS NEAR THE PALO ALTO WATER QUALITY CONTROL PLANT
IN SOUTH SAN FRANCISCO BAY: 1999-2001

\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_

Carlos Primo C. David, Samuel N. Luoma, Cynthia L. Brown, Daniel J.
Cain,

Michelle I. Hornberger and Irene R. Lavigne

**ABSTRACT**

\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_

This report presents trace element concentrations analyzed on samples of
fine-grained sediments and clams (*Macoma balthica*) collected from a
mudflat one kilometer south of the discharge of the Palo Alto Regional
Water Quality Control Plant in South San Francisco Bay. This report
serves as a continuation of

the Near Field Receiving Water Monitoring Study which was started in
1994. The data for 1999 -- 2001 are interpreted within that context.
Generally, metal concentrations in both sediments and clam tissue
samples have been within the range of values produced by seasonal
variability. Copper and zinc, however, display a continued decrease,
recording the lowest winter maxima concentrations in both sediment and
tissue samples in 2001. Yearly average of bioavailable copper, zinc and
silver concentrations in 1999-2001 are some of the lowest recorded since
monitoring began in 1975. A slight increase in mercury in sediments and
selenium in tissue in early 2001 are also observed. These enrichments
are believed to be mainly caused by hydrogeologic processes affecting
the area although only continued sampling will confirm whether
anthropogenic sources influence the concentrations of these elements.

**INTRODUCTION**

Sampling sediments and benthic organisms in an estuary is a common
method used to determine spatial distributions and temporal trends of
metal contamination. Sediment particles strongly bind metals,
effectively removing them from solution. As a result, sediments may
retain metals released to the environment. Thus, concentrations of
metals in sediments serve as a record of metal exposure in an estuary,
with at least some integration over time. Fluctuations in the record may
be indicative of changes in anthropogenic releases of metals into the
environment.

Metals in sediments are also indicative of the level of metal exposure
of benthic animals in contact with bottom sediments and suspended
particulate materials. However, the route through which organisms
assimilate bioavailable sediment-bound metal is not well understood. In
order to better estimate bioavailable metal exposures, the tissues of
the organisms themselves may be analyzed for trace metals. Benthic
organisms concentrate most metals to levels higher than those that occur
in solution, and therefore, the record of tissue metal concentrations
can be a more sensitive indicator of anthropogenic metal inputs than the
sediment record. Different species concentrate metals to different
degrees. If one species is analyzed consistently, the results can be
employed to indicate trace element exposures to the food web of the
organism. For example, silver (Ag), copper (Cu) and selenium (Se)
contamination, originally observed in clams (*Macoma balthica*) at the
Palo Alto mudflat, was later also found in diving ducks, snails, and
mussels from that area (Luoma et al., USGS, unpublished data).

Because of the proven value of the above approaches for monitoring near
field receiving waters, the California Regional Water Quality Control
Board (RWQCB) has described a Self Monitoring Program, with its
re-issuance of the National Pollutant Discharge Elimination System
(NPDES) permits for South San Francisco Bay dischargers, that includes
specific receiving water monitoring requirements. One of the
requirements is for inshore monitoring of metals and other specified
parameters using the clam *Macoma balthica* and fine-grained sediments.
The protocols should also be compatible with or complement the Board\'s
Regional Monitoring Program. Monitoring efforts are to be coordinated
with the U. S. Geological Survey\'s (USGS) 22 years of previous data
collected from the site south of the Palo Alto discharge site.

**PURPOSE**

The purpose of this study is to present trace metal concentrations
observed in sediments and clams at an inshore location in South San
Francisco Bay. These data and those collected in earlier studies (Luoma
et al., 1997) will be used to approach the following objectives:

-   Provide data to assess seasonal and year-to-year trends in trace
    element concentrations in sediments and clams in receiving waters
    near the Palo Alto Regional Water Quality Control Plant (RWQCP) as
    designated in the RWQCB\'s Self-Monitoring Program guidelines.

-   Present the data within the context of historical changes inshore in
    South Bay and within the context of other locations in San Francisco
    Bay published in the international literature.

-   Coordinate inshore receiving water monitoring programs for Palo Alto
    and provide data compatible with relevant aspects of the Regional
    Monitoring Program. The near field data will augment the Regional
    Monitoring Program as suggested by the RWQCB.

-   Provide data which could support other South San Francisco Bay
    issues or programs such as development of sediment quality
    standards.

# STUDY SITE

The Palo Alto site (PA) is located one kilometer south of the intertidal
discharge point of the Palo Alto RWQCP (Figure 1). The data reported
here are from samples collected in January 1999 through December 2001.

Spatial distributions of metal concentrations near the Palo Alto RWQCP
site were described by Thomson et al. (1984) (also reported by Luoma et
al., 1991; 1992; 1993; 1995; 1996; 1997; 1998; Wellise et al., 1999).
The RWQCP appeared to be the primary source of the elevated metal
concentrations at the PA site in spring, 1980, based upon spatial and
temporal trends of Cu, Ag and Zn in clams and sediments (Thomson and
others, 1984; Cain and Luoma, 1990). Metal concentrations in sediments
and clams (especially Cu and Ag) have declined substantially since the
original studies, as more efficient treatment processes and source
control were employed that significantly reduced metal discharges from
the treatment plant (Hornberger et al., 2000). However, frequent
sampling within a year was necessary to characterize those trends since
there was significant seasonal variability (Cain and Luoma, 1990; Luoma
et al., 1985). This report characterizes trends for 1999-2001, employing
the methods described in the succeeding section.

Previous reports (Luoma et al., 1995; 1996; 1997; 1998; Wellise et al.,
1999) included another study area in addition to the Palo Alto sampling
site. This area was located in a region that was influenced by discharge
from the San Jose/Santa Clara Water Pollution Control Plant. Samples
were collected from this site from 1994 to September 1999. Reference to
the SJ site allowed differentiation of local and regional long-term
metal trends.

**METHODS**

The PA site samples were collected from the exposed mudflat at low tide,
with hand and shovel. Sediment samples were scraped from the surface
oxidized layers (1 ‑2 cm) of mud. Thus, samples represent recently
deposited sediments, or sediments affected by recent chemical reaction
with the water column. Sediment samples were immediately taken to the
laboratory and sieved through a 100 μm polyethylene mesh with distilled
water to remove large grains that might bias interpretation of
concentrations. The mesh size was chosen to match the largest grains
typically found in the digestive tract of *Macoma balthica*. To provide
a measure of bulk sediment characteristics at a site (and thus provide
some comparability with bulk sediment determination such as those
employed in the Regional Monitoring Program -- San Francisco Estuary
Institute (SFEI), 1997), the percent of the sediment mass that passed
through the sieve was determined. This fraction is termed percent
silt/clay in the following discussion. Previous studies have shown
little difference between metal concentrations in sieved and unsieved
sediments when silt‑clay type sediment is dominant at a station.
However, where sand-size particles dominate the bed sediment,
differences can be substantial. Spatially and temporally, sediments in
extreme South San Francisco Bay can vary in their sand content (Luoma et
al., 1995; 1996; 1997; 1998; Wellise et al., 1999; also see SFEI, 1997).
Where sand content varies, sieving reduces the likelihood that
differences in metal concentration are the result of sampling sediments
of different character. All sediment data reported herein were
determined from the fraction that passed through the sieve (\< 100 μm).
Some differences between the USGS and the Regional Monitoring Program
results (SFEI, 1997) reflected the bias of particle size on the latter's
data.

The fraction of sediment that did not pass through the sieve was weighed
and the percentage of the bulk sample was determined to assess percent
sand and percent silt/clay in the sediment. The \<100 μm fraction was
dried at 60^o^C, weighed, and then measured into 0.4 to 0.6 gram
aliquots in replicates for analysis. The samples were again dried at
60^o^C before re-weighing and extraction. The replicate subsamples were
digested for near-total metal analysis by refluxing in 10 ml of
concentrated nitric acid until the digest was clear. This method is
comparable with the recommended procedures of US Environmental
Protection Agency and with the procedures employed in the Regional
Monitoring Program. It also provides data comparable to the historical
data available on San Francisco Bay sediments. While near-total analysis
does not result in 100% recovery of all metals, recent comparisons
between this method and more rigorous complete decomposition show that
trends in the two types of data are very similar (Hornberger et al.,
1999). After decomposition, samples were evaporated until dry and
reconstituted in dilute (5 percent) hydrochloric acid for analysis. The
hydrochloric acid matrix was specifically chosen because it mobilizes
silver (Ag) into solution through the creation of Ag‑chloro complexes.
Sediment samples were also subjected to a partial weak acid extraction
in 0.5N Hydrochloric acid (HCl), as a crude chemical estimate of
bioavailable metal. These subsamples were extracted for 2 hours with 12
ml of acid at room temperature. The extract was pressure filtered
through a 0.45 μm membrane filter before analysis. Total organic carbon
was determined by difference between total carbon and carbonate, using a
total combustion carbon analyzer. Salinity was determined for surface
water and the mantle water of clams at the time of collection using a
refractometer. Mantle water and surface water salinity were typically
within 1 ppt (‰) of each other.

The deposit feeding clam *Macoma balthica* was collected simultaneously
with the sediment samples. More than 60 individuals were collected on
each sampling occasion. The range of sizes (shell length) was maximized
by intensive field sampling, where possible. Animals were returned to
the laboratory and held for 48 hours in ocean water diluted to the
ambient salinity at the time of sampling, to depurate undigested
material from their digestive tracts. After depuration, the individual
clams were separated into 1mm size classes. Soft tissues from all of the
individuals in a size class were collected to constitute a single sample
for analysis. Samples for each date were thus composed of six to
thirteen replicate composites, with each composite consisting of 3 to 15
animals of a similar shell length. Animal tissue samples were dried,
weighed and refluxed in concentrated nitric acid until the digest was
clear. Digests were then dried and reconstituted in dilute (5 percent)
hydrochloric acid for trace metal analysis.

Metals analysis was conducted by using Inductively Coupled Plasma
Optical Emission Spectroscopy (ICP-OES). Mercury (Hg) and Se were
determined in both sediment and clam tissues by Hydride Atomic
Absorption Spectrophotometry. Mercury subsamples were digested at 100^o^
C in aqua regia, re-digested in 10 percent nitric acid plus potassium
dichromate and then reduced at the time of the hydride analysis.
Selenium subsamples were digested in concentrated nitric and perchloric
acids at 200^o^C and reconstituted in hydrochloric acid.

All glassware and field collection apparatus used were acid washed,
thoroughly rinsed in ultra-clean deionized water, dried in a dust-free
positive pressure environment, sealed and stored in a dust free cabinet.
Quality control was maintained by frequent analysis of blanks, analysis
of National Institute of Standards and Technology (NIST) standard
reference materials (tissues and sediments) with each analytical run,
and internal comparisons with prepared quality control standards. A full
QA/QC plan is available upon request. Analyses of NIST reference
materials (oyster tissue, San Joaquin soils) were within an acceptable
range of certified values reported by NIST or were consistent where the
nitric acid digest did not completely decompose the sediment samples
(Table 1 and 2). High recoveries for Cd have been observed for the
sediment standard. As a result, Cd in sediments for 2000 and 2001 will
not be reported until this instrument interference is corrected or until
the samples are re-run with conventional atomic absorption spectrometry
(AAS). Tables 3-7 show monthly values for all analyses for both sediment
and clam samples.

Appendix 1 shows the details of the analyses of sediments. Appendix 2
lists the details of metal analyses of clam tissues. Statistical data
indicates size influences on tissue concentrations, and content
calculations are reported with their corresponding summary statistics.
Analytical data and detection limits also are given for each sample to
aid in verification of peaks and trends.

**RESULTS AND DISCUSSION**

Figure 2 shows the surface water salinity on the dates that samples were
collected at the Palo Alto site. Compared to the previous 5 years, high
salinity for 1999 and 2001 were recorded indicating relatively low
runoff during winter. Salinity did not go below 20 ppt in 2001, the
highest wintertime salinity in the past six years. Only 1994 suggested a
comparable pattern of low freshwater inflow during the normal wet
season. Maximum salinities for 1999-2001 were comparable to other peak
salinities in the past five years, with 1994 and 1997 still showing the
highest salinity maxima recorded within the past 8 years.

Sediment characteristics of the samples are shown in Figure 3. Percent
silt/clay in sediments indicates particle size distributions before
sediments were sieved. At Palo Alto, percent silt/clay typically varied
from 50 - 100% by weight. Aluminum (Al) concentrations changed directly
with the proportion of clay-size (very fine) particles within the 100 μm
fraction of the sediment (after sieving). Iron (Fe) concentrations were
probably influenced by a combination of seasonal inputs from the
watershed and other sediment processes. Percent silt/clay, Al and Fe
tended to follow a seasonal cycle of relative increases early in the
year then declining to a minimum by September or October. The seasonal
trend, especially for Al and Fe concentrations, was typical of that
reported earlier for this site by Thompson-Becker et al. (1985). Those
authors suggested that fine sediments, accompanied by high Al and Fe
concentrations, are dominant during the period of freshwater input (low
salinities through April), reflecting annual terrigenous sediment inputs
from runoff. Coarser sediments dominated later in the year because the
seasonal diurnal winds progressively winnow the fine sediments into
suspension through the summer. All indicators showed winnowing had a
greater effect in 2001 than in other years.

The seasonal cycles of chromium (Cr), vanadium (V) and nickel (Ni) in
sediments are shown in Figure 4. These elements are strongly enriched in
some geologic formations within the watershed. The pattern of seasonal
change for these metals in 1999 through 2001 were typical of earlier
years, with the highest concentrations early in the year (winter maxima)
and the lowest concentrations in September-November. In North San
Francisco Bay, studies of sediment cores indicated that concentrations
of these elements similar to that reported here were derived from
natural geologic inputs (Hornberger et al., 1999). However, Cr and Ni
also occur in the effluents of the PA RWQCP. The seasonal variability
and the similarities among Cr, Ni and V continued to suggest that
hydrogeologic processes were the predominant influence on concentrations
of these elements.

Copper maintained its seasonal cycling signature, however, a decrease in
its total extract concentration in 2001 was evident (Figure 5). Winter
maxima peaks were at 41 μg/g as opposed to 50-58 μg/g in previous years.
For the first time, Cu in sediments for 2000 and 2001 has fallen well
below the effects range-low (ERL) guidelines set by the National Oceanic
and Atmospheric Administration (Long et al., 1995). Long et al. (1995)
defined values between ERL (Effects Range-Low) and ERM (Effects
Range-Median) as concentrations that are occasionally associated with
adverse effects (21 - 47% of the time for different metals). Values
greater than the ERM were frequently associated with adverse effects
(42% - 93% of the time for different metals). It must be remembered,
however, that these effects levels were derived mostly from bioassay
data and are not literally accurate estimates of sediment toxicity. The
decrease in total Cu in sediments was not so much reflected in the
HCl-extract trend although the lowest concentration since 1994 was
recorded in September 2001.

Figure 6 shows total and HCl-extractable Zn. Zinc showed an evident
decrease in its concentration starting in November 2000, with the 2001
winter maxima falling well below the Zn ERL. This trend was recorded for
both total and HCl-extractable Zn. Concentrations of HCl-extractable Ag
in sediments did not show the 2000-2001 decrease and maintained the
range of concentration that was perceived to be attributable to seasonal
cycling of the element (Figure 7). This range was above the established
concentration for uncontaminated sediments in San Francisco Bay
(Hornberger et al., 1999) but well below the Ag ERL. Sediment
concentrations of cadmium (Cd) were slightly elevated from 1997 through
1999 compared to earlier years; although overall concentrations were
lower compared to projected biological effects thresholds (1.2 μg/g)
(Long et al., 1995) (Figure 8). Also, there appears to be a general
decreasing trend over the last three years.

Mercury concentrations in Palo Alto sediment remained consistent with
earlier years at an enrichment level typical of the Bay as a whole
(0.2 - 0.4 μg/g) (Figure 9). Concentrations of Se in sediments showed a
maximum in February 1999 that was more elevated than the corresponding
seasonal maxima in previous years. This was followed by relatively low
concentrations in 2000 and 2001. The maximum Se concentration observed
in PA sediment was comparable to the highest concentrations observed in
sediments anywhere in the San Francisco Bay (Hornberger et al., 1999).

Annual mean concentrations (on a calendar year basis) of Cu and Ag in
*Macoma balthica* are shown in Figures 10 and 11. Exposures to Cu and
Ag, as reflected in clam tissues have been of special interest due to
the high concentrations that these metals recorded in the 1970s and
1980s. Trends in these two metals at Palo Alto were lower throughout the
1990s than in the years prior to 1988. The previous minimum
concentrations were observed in 1991, but a five-year period of slightly
increased concentrations followed. Since 1997, both Cu and Ag
concentrations have shown a period of decline, with 2001 concentrations
among the lowest observed during the 20-year period of study.

Copper concentration in clams displayed a seasonal signal, however, the
last four years of data evidently showed a decrease in winter maxima
(Figure 12). This trend seemed to have started in mid-1997 wherein the
range of Cu concentrations decreased to only 17-48 μg/g as opposed to
21-100 μg/g in previous years. Silver also showed the same depressed
winter maxima which started in 1997 (Figure 13).

Figures 14-16 show Zn, Cr and Ni concentrations in *Macoma balthica*.
Wellise et al. (1999) observed that the metals trends in Palo Alto clam
samples were similar to those from the San Jose site, suggesting that
regional-scale processes may be more important than treatment plant
inputs in controlling seasonality and bioavailability of these elements.
The seasonality signal continued in the data from 1999 to 2001 wherein
the lowest Cr, Ni, and Zn were observed during Spring (May-June),
whereas the maxima typically occurred during winter (December-March).
However, Cr and Ni displayed narrower concentration ranges in their
1999-2001 annual cycles due to a slightly depressed winter maxima when
compared with previous years. Conversely, one of the highest Zn levels
recorded was in March 2000 although the lowest Zn concentration in the
entire time series was in November of the same year.

Selenium concentrations in sediments and clam tissue did not show
similar trends (Figure 17). While a slight decrease in Se average
concentration in sediment was observed for 2000-2001, concentrations in
clams varied from \<3 μg/g to 7 μg/g, with the highest concentration
recorded in January 2001. The cause for the increase in Se
concentrations in clam samples is still unclear at this point. On the
other hand, Hg in clam samples remained within the concentration range
of the element (0.15-0.36 μg/g) since a recorded decrease in mid-1996
(Figure 18).

Figure 19 shows the condition index for clams for the period of 1988
through 2001. Condition index (CI) is a measure of physiological
\"fatness\", the tissue weight of a clam of a given length. It is an
index of the clams\' well-being and indicative of how well clams prepare
for the seasonal reproductive cycle. Seasonally, a clam of a given shell
length will add glycogen and weight as it prepares for reproduction.
That glycogen is metabolized and weight is lost during and after
reproduction. Stress caused by pollutant exposure, salinity stress or
lack of food, can consume energy, affect net glycogen accumulation, and
reduce condition index.

The condition index for 1999 and 2001 were similar to the period from
1994 through 1996 and even slightly higher values observed in 2000
(Figure 19). High CI in 1997 and 1998 at PA coincided with reduced
concentrations of Cu and Ag, as well as a large phytoplankton bloom
occurrence (Wellise et al., 1999). Moreover, while CI maxima were
typically within the range of values observed in previous years, the
annual minima for 1999-2001 have been the highest in the 14-year
dataset. This may be suggestive of further improvement in clam
physiology, however, further investigation is necessary to understand
the dynamics of food availability and condition to interpret this
observation. A simple correlation between maximum condition index and
the preceding months' maximum metal exposure was not significant. Still,
the data distribution (Figure 20) raised the possibility that Cu
concentrations above 80 - 90 μg/g might affect growth in the bivalves.
The 1999-2001 data were consistent with this relationship since the
copper concentrations are below the threshold where it has a probable
effect on habitat conditions.

Frequent sampling was essential for characterizing ambient metal
concentrations in the environments in the vicinity of the outfall.
Monitoring studies could not always unambiguously determine the causes
of the trends in metals concentrations in either sediments or clams. The
value of monitoring was to describe trends, to identify previously
undocumented phenomena, and to raise otherwise unrecognized hypotheses
that might guide detailed explanatory studies. Signals coming from
anthropogenic sources overprinted onto natural annual and inter annual
variability could only be recognized through the interpretation of time
series data. For many elements of regulatory interest, including Cr, V,
Ni, and Zn, regional scale factors appeared to influence sedimentary and
bioavailable concentrations, although this may not be completely
accurate in all years. The decrease in Cu and Ag concentrations in clam
and sediment samples reflected the continued decrease in these metals'
loading from the treatment plant. However, other variables that may
contribute to this decline in concentration such as a decrease in
precipitation for 1999-2001 should still be investigated.

**REFERENCES CITED**

Cain, D. J. and Luoma, S. N., 1990, Influence of seasonal growth, age
and environmental exposure on Cu and Ag in a bivalve indicator, *Macoma
balthica* in San Francisco Bay: Marine Ecology Progress Series 60, p. 45
‑ 55.

Hornberger, M. I., Luoma, S. N., Van Geen, A., Fuller, C. C., and Anima,
R. 1999, Historical trends of metals in the sediments of San Francisco
Bay, California. Marine Chemistry 64, p. 39-55.

Hornberger, M.I., Luoma, S. N., Cain, D., Parchaso, F., Brown, C.,
Bouse, R., Wellise, C.J., Thompson, J., 2000, Bioaccumulation of metals
by the bivalve *Macoma balthica* at a site in South San Francisco Bay
between 1977 and 1997: Long-term trends and associated biological
effects with changing pollutant loadings. U. S. Geological Survey Open
File Report 99-55. Menlo Park, California.

Long, E. R., MacDonald, D. D., Smith, S. L., and Calder, F. D., 1995,
Incidence of adverse biological effects within ranges of chemical
concentrations in marine and estuarine sediments: Environmental
Management, v. 19, p. 81 - 97.

Luoma, S. N., Cain, D. J., Brown, C. and Axtmann, E. V., 1991, Trace
Metals in Clams (*Macoma balthica*) and sediments at the Palo Alto
Mudflat in South San Francisco Bay: April, 1990 - April, 1991. U. S.
Geological Survey Open File Report 91-460. Menlo Park, California. 47pp.

Luoma, S. N., Cain, D. J., Brown, C. and Hornberger, M., 1992, Trace
Metals in Clams (*Macoma balthica*) and sediments at the Palo Alto
Mudflat in South San Francisco Bay: May 1991 - May 1992. U. S.
Geological Survey Open File Report 92-456. Menlo Park, California. 51pp.

Luoma, S. N., Cain, D. J., Brown, C. and Hornberger, M., 1993, Trace
Metals in Clams (*Macoma balthica*) and sediments at the Palo Alto
Mudflat in South San Francisco Bay: June 1992 - June 1993. U. S.
Geological Survey Open File Report 93-500. Menlo Park, California. 52pp.

Luoma, S. N., Cain, D. J., Brown, C. and Hornberger, M., 1995, Near
Field Receiving Water Monitoring of Trace Metals in Clams (*Macoma
balthica*) and sediments near the Palo Alto and San Jose/Sunnyvale Water
Quality Control Plants in South San Francisco Bay: June 1993 - October
1994. U. S. Geological Survey Open File Report 95-299. Menlo Park,
California. 83pp.

Luoma, S. N., Cain, D. J., Brown, C., Hornberger, M., and and Bouse, R.
1996, Near Field Receiving Water Monitoring of Trace Metals in Clams
(*Macoma balthica*) and sediments near the Palo Alto and San
Jose/Sunnyvale Water Quality Control Plants in South San Francisco Bay:
December 1994 - December 1995 U. S. Geological Survey Open File Report
96-203. Menlo Park, California. 90pp.

Luoma, S. N., Cain, D. J., Brown, C., Hornberger, M., and Bouse, R.
1997, Near Field Receiving Water Monitoring of Trace Metals in Clams
(*Macoma balthica*) and sediments near the Palo Alto and San
Jose/Sunnyvale Water Quality Control Plants in South San Francisco Bay:
1996 U. S. Geological Survey Open File Report 97-585. Menlo Park,
California. 91pp.

Luoma, S. N., Wellise, C, Cain, D. J., Brown, C., Hornberger, M., and
and Bouse, R. 1998, Near Field Receiving Water Monitoring of Trace
Metals in Clams (*Macoma balthica*) and sediments near the Palo Alto and
San Jose/Sunnyvale Water Quality Control Plants in South San Francisco
Bay: 1997 U. S. Geological Survey Open File Report 98-563. Menlo Park,
California. 88pp.

San Francisco Estuary Inst. 1997, RMP, Regional Monitoring Program for
Trace Substances: 1996. Richmond, CA. 349 pp.

Thomson, E. A., Luoma, S. N., Johansson, C. E., and Cain, D. J., 1984,
Comparison of sediments and organisms in identifying sources of
biologically available trace metal contamination: Water Research, v. 18,
p. 755 ‑ 765.

Thomson-Becker, E. A., and Luoma, S. N., 1985. Temporal fluctuations in
grain size, organic materials and iron concentrations in intertidal
surface sediment. Hydrobiologia, v. 129, p. 91-109.

Wellise, C., Luoma, S. N., Cain, D. J., Brown, C., Hornberger, M., and
Bouse, R. 1999, Near Field Receiving Water Monitoring of Trace Metals in
Clams (*Macoma balthica*) and sediments near the Palo Alto and San
Jose/Sunnyvale Water Quality Control Plants in South San Francisco Bay:
1998 U.S. Geological Survey Open File Report 99-455. Menlo Park,
California. 101pp.

**APPENDIX 1.** Metal concentrations determined by ICP-OES in sediments
collected at the Palo Alto mudflat. Each monthly collection is reported
on a separate page. Concentrations observed in the reconstituted samples
or extracts (in micrograms per milliliter or μg/ml) are reported at the
top of each page, along with the sediment weight and dilution factor.
The latter are employed to determine concentrations in sediments
(reported as microgram per gram dry sediment or μg/g). Replicate
subsamples were analyzed from each collection. Mean and standard
deviation for the replicate samples are reported for the total and
hydrochloric acid extracts. Samples that were below detection limit are
denoted as "bd".

Grain size data (p. 46) as well as TOC analyses (p. 47) and
concentrations of Hg and Se in surface sediments (p. 63) are reported in
separate summary tables.

**APPENDIX 2.** Metal concentrations in the clam *Macoma balthica*
collected at the Palo Alto Mudflat. Each monthly collection is reported
on two pages. The first page contains summary statistics:

Mean concentrations in microgram per gram dry tissue weight (μg/g).

STD is the standard deviation of the mean.

SEM is the standard error of the mean.

CV percent is the coefficient of variation.

r wt x \[\] is the correlation coefficient for the concentration versus
weight correlation for each element.

X 100mg is the concentration interpolated from the above regression for
a 100 mg animal.

r l x \[\] is the correlation coefficient for the concentration versus
shell length regression.

X 20 mm and X 25 mm are concentrations interpolated from the regression
for 20mm and 25 mm animals.

Content (a measure of metal bioaccumulation that is independent of mass)
is also shown for 20 and 25 mm animals, as is the weight determined for
animals of 15 mm and 20 mm shell length.

The second page for each month shows the analysis of each composite
sample, the number of animals composited in each, concentration as
calculated from sample dry weight and the dilution factor and the metal
content for each sample.