Daniel Watson, Lisa Weetman, Donald Arnold, Charles Allen, Kenneth Lee, James Powars,

Joe Thiesen, Hannah Truong, and Robert Wandro

Environmental Services Department, City of San Jose

4245 Zanker Road, San Jose, CA 95134

Phone: (408) 945-3739; Fax: (408) 934-0476

In February of 1997 an ambitious sampling program was initiated by the City of San Jose to characterize water quality parameters at twelve sites in San Francisco Bay south of the Dumbarton Bridge. The purpose of this study was to describe spatial and temporal variability in an enclosed water body for trend analysis and modeling. The study design incorporated the use of "clean techniques" to monitor trace metals, microbiological testing, and general water quality measurements. Sampling was conducted biweekly. Ambient water concentrations in the extreme South Bay of metals tested decreased on a gradient northward toward the Central Bay. Total mercury values were highest in Coyote and Guadalupe Creeks, possibly originating from abandoned cinnabar mines. Microbiological samples were highest in these two creek systems; both areas harbor bird rookeries. Levels of most total metals measured correlated well with Total Suspended Solids, and a to lesser degree, with Total and Dissolved Organic Carbon. High total metals correlated well with wind and storm events. Dissolved metals concentrations showed little seasonal variability and a decreasing spatial trend from sources of in-put, toward the central portion of the San Francisco Bay, which is influenced by oceanic water.

Over 100 years ago a chemist named Forchhammer postulated that it is not the quantity of elements that rivers pour into the sea which determines the chemical elements in seawater. He theorized that concentrations are inversely proportional to the facility with which the elements in seawater are made insoluble by general chemical actions in the sea (Strumm and Morgan 1996). Estuaries are mixing zones where chemicals come to equilibrium between their soluble and insoluble forms. As such, it is important to study the interaction of chemicals in bays and estuaries.

The State of California’s Regional Basin Plan for San Francisco Bay (SFRWQCB 1995) recognized that the South San Francisco Bay is a "unique water-quality limited, hydrodynamic and biological environment that merits continued special attention" and that "site-specific objective are absolutely necessary in this area." The State listed South San Francisco Bay as an impaired water body on its 1996 303(d) and TMDL Priority List, primarily due to high total metal concentrations. Two studies performed in the South Bay (S.R. Hansen and Associates 1992; CH2M Hill et al. 1991) attempted to address the issue of toxicity from copper and/or nickel in Bay waters and establish Water Effect Ratios (WERs) for these two metals. A later study (City of San Jose 1997) measured ambient concentrations of Cu and Ni in South San Francisco Bay waters and performed biweekly copper WER tests on the blue mussel, Mytilus edulis, from January 1996 through March 1997.

Total nickel and copper concentrations frequently exceed water quality objectives during the dry season (May to October) when flows from Publicly Owned Treatment Works (POTWs) dominate in-put to the South Bay (SFEI 1993, 1994, 1995, 1996; and City of San Jose 1997). This fact has lead some people to conclude that the sources of these metals in the extreme South Bay are mainly from POTWs. Dissolved Cu and Ni, however, did not show large concentration peaks or seasonal fluctuations (City of San Jose 1997). Most of the Cu and Ni discharged from San Jose/Santa Clara Water Pollution Control Plant (SJ/SC WPCP) are dissolved, 96 and 98%, respectively.

The City of San Jose initiated a monitoring study to elucidate spatial and temporal metal loading in the area south of the Dumbarton Bridge (Figure 1). A team from the City of San Jose’s Environmental Services Department designed a monitoring study to characterize the deep channels and mudflats and to detect non-point source stream concentrations. Sampling began in February 1997. Results will be used for model validation as the Regional Board prepares a Total Maximum Daily Load (TMDL) study for the South Bay.

To facilitate comparisons with data produced by the Regional Monitoring Plan (RMP), the San Jose team adopted techniques employed by the RMP. Samples for trace metal analysis were collected employing EPA Method 1669. The current San Jose study coordinated three sampling events in 1997 to coincide with RMP cruises in the South Bay. In addition, the RMP cruises took samples in the South Bay to be processed by the City of San Jose laboratory as an additional inter-comparative check. Although the data from the 1997 RMP is currently not available, results of the comparison will be published in the 1997 Annual RMP Report.

Ten stations (SB01-SB10) were selected in the extreme South Bay (south of Dumbarton Bridge) to represent both channel and mudflat locations. Previous studies had sampled channel stations, but overlooked mudflat sites. Two other stations, Standish Dam (SB11) and Alviso Marina (SB12), were added to monitor water flowing into the Bay from Coyote and Guadalupe Creeks, respectively. These two stations were sampled from the shore. Sampling frequency was biweekly in order to assess temporal change over seasons. Sampling times were varied to better assess tidal influence on metal concentrations. The City’s previous study (City of San Jose, 1997) sampled South Bay stations only at high tide.

Certain station locations were selected to promote comparisons with previous studies. Four of the ten South Bay stations in this study were at the same location to RMP sampling sites. Two stations, also, corresponded to locations in the City’s WER study (City of San Jose, 1997). Station SB01 in the current study (located 0.85 nautical miles north of the Dumbarton Bridge) corresponds to BA30 of the RMP sites and DBN in the City’s previous study. Station SB02 corresponds to BA20 for the RMP. Station SB03 corresponds to BA10 of the RMP and CC in the City’s previous investigation. Station SB04 is equivalent to the RMP station C-3-O. It should be noted that SB04 is the station closest to the convergence of Coyote Creek and Artesian Slough, which can be highly influenced by water discharged from the SJ/SC WPCP. Also, station SB05 of the present study corresponds to the Local Effect Monitoring (LEM) site for the cities of Sunnyvale and San Jose. The US Geological Survey in Menlo Park has monitored sediment and tissue (of the clam Macoma balthica) pollutant levels at this LEM site since 1993.

Sampling was performed aboard a seventeen foot Boston Whaler. Water was collected at a depth of approximately one meter using Teflon and C-Flex^® tubing with a peristaltic pump. A deep-cycle marine battery powered the peristaltic pump, which was encased with a voltage converter in a water resistant polyethylene housing.

Total and dissolved trace metals were collected using "clean techniques" in triplicate 500 ml HDPE bottles (3X HNO₃ rinsed; 3X NannoPure water rinsed) for Cu, Ni, and Se. Single samples were collected in 1L Teflon (PTFE) bottles for total mercury. Dissolved metal samples were filtered in situ by drawing water through 5.0m and 0.45m filters (Micron Separation, Inc.) connected in series. Filters were used repeatedly with ample flushing between stations and were replaced when flow diminished. Other water quality parameters measured were Total Suspended Solids (TSS), Total Dissolved Solids (TDS), Total Organic Carbon (TOC), Dissolved Organic Carbon (DOC), salinity (S%), and conductivity. Microbiological samples were collected in two-liter sterile polyethylene jugs for total coliform, fecal coliform, and enterococcus. Samples were maintained at 4^oC in ice chests and returned to the laboratory within four hours of sampling.

Samples were preserved at the laboratory using ultra pure nitric acid (pH below 2). Copper and nickel were analyzed using a modification of EPA Method 1640. This technique involves precipitation of Cu & Ni by cobalt-pyrrolindinedithiocarbamate followed by filtration and detection by Inductively Coupled Plasma – Mass Spectroscopy (ICP-MS). Selenium was analyzed using a combination of EPA Method 270.2 and 270.3. Selenium hydride was generated and concentrated on an iridium coated graphite tube. The concentrated selenium was then vaporized on the tube and detected by atomic absorption spectroscopy. Method detection level for selenium was 0.002 m g/L. Mercury was sampled in one-liter Teflon bottles which were acid cleaned and filled with 0.1% HCl until time of sampling. Bottles were filled completely with the sample to minimize headspace and preserved in 0.1% HNO₃ . Mercury was analyzed using EPA Method 245.2 modified for gold amalgamation concentration on a Perkin-Elmer FIMS system. The method detection level for mercury was 0.0007m g/L.

Samples for Cu, Ni, and Se were sent to a commercial laboratory in Washington when the City’s laboratory was unable to handle the backlog (June to December, 1997). This commercial laboratory used similar methods. Results were verified with standard reference materials, spikes, and duplicates.

Total Organic Carbon (TOC) and Dissolved Organic Carbon (DOC) were analyzed on a Shimadzu 5000 Carbon Analyzer using Standard Methods, 18^th edition, Method 5310B and ASTM D-2579-93. Total Suspended Solids (TSS) were analyzed using Standard Methods, 18^th edition, Method 2540D. Total Dissolved Solids (TDS) were analyzed using Standard Methods, 18^th edition, Method 2540C. Conductivity was analyzed using Standard Methods, 18^th edition, Method 2510B. Salinity was measured with a Reichert temperature compensated refractometer to the nearest 0.5 part per thousand (S^O/_OO).

Microbiological assessment was done in conjunction with the San Jose/Santa Clara WPCP chlorine reduction study. Baseline data existed for bacteria in the South Bay from a Receiving Water Monitoring survey performed as a requirement of the City of San Jose’s NPDES permit in the late 1980’s and early 1990’s. Several years had elapsed, however, since that sampling ended in 1994.

Total coliform bacteria were assessed using Standard Methods, 18^th edition, Method 9221C. Fecal coliforms were quantified using Standard Methods, 18^th edition, Method 9221E. Enterococcus microorganisms were assayed by Standard Methods, 18^th edition, Method 9230B. All units are expressed in Most Probable Number (MPN)/100 ml.

Blanks. To confirm absence of background contamination at parts per billion levels, numerous blanks were required. Blanks were used to assess contamination caused by sample bottles, NannoPure water, day-to-day field equipment, field sampling, and filtration. Trace metal blanks were analyzed without the concentration step of cobalt precipitation. NannoPure water was also sampled for blanks of TOC/DOC and TSS/TDS. Bacteriological equipment and field blanks were also taken for each sampling event to characterize biological contaminants that might be retained and passed to the next sample.

Standard Reference Material. With each sampling event a standard reference material (SRM) was submitted as a blind sample. The standard reference material, CASS-3, (Canadian Research Council, Coastal Seawater) was preferred because of the laboratory’s need to analyze low levels of metals in site water.

Spikes. Spiking of certain samples was performed as a quality assurance check when samples were sent to a commercial laboratory. This step was to verify consistency with the City of San Jose Environmental Services Department laboratory results and percent recovery.

Replicate Sampling. Both total metals and dissolved metals were taken in triplicate at each station in order to have complete confidence that values detected were not anomalous. One station (SB10) was selected to perform duplicate sampling for TSS/TDS, TOC/DOC, and mercury, which were otherwise represented by one sample at the other eleven stations.

Inter-Study Comparisons. Coordinated with previous and on-going sampling studies discussed above were part of this monitoring Quality Assurance Plan.

Mean total copper concentrations (Figure 2) was highest in Coyote (SB11) and Guadalupe Creeks (SB12) upstream from the South Bay sites. These two stations are located on the right side of the graphs (light gray bars). The series of six stations on the left hand of the graphs (dark bars) represent channel stations. Stations Sb07-SB10 (four light gray bars on the right side of the graphs) represent mudflat stations around the periphery of the South Bay. Stations SB04 and SB05 (in the lower section of Coyote Creek) both had mean total copper concentrations approaching the creeks of nearly 11 m g/L. Mean total copper in the San Jose/Santa Clara effluent (center dark bar) was 4.3 m g/L. Non-point source in-put from the creeks and re-suspension appear to be the main origin of total copper in lower Coyote Creek, showing a progressive decrease in concentration from south to north in the study site. Standard error bars for the creek stations were larger because of the variability in seasonal flows and sediment loads.

Mean dissolved copper concentrations remained fairly consistent (between 2.3-2.9 m g/L) from the creeks to the station north of the Dumbarton Bridge (SB01). By comparison, the mean dissolved copper concentration in the SJ/SC WPCP final effluent was 3.9 m g/L. Most (nearly 92%) of the copper in the final effluent is in the dissolved phase compared to South Bay sites which had dissolved-to-total ratios of 51% or less. No significant elevation in mean dissolved copper is evident in Coyote Creek downstream of the confluence with Artesian Slough. In fact, there was a decrease in the dissolved-to-total ratios at stations immediately downstream from the SJ/SC WPCP (stations SB04 and SB05). This decrease in ratios may be due primarily to higher total copper concentrations associated with particles transported down Coyote Creek.

Since the South Bay is shallow with a large tidal prism of approximately 1.8 billion cubic feet (CH2M HILL. 1990), water column metals concentrations are greatly affected by re-suspension of bottom sediments (RMA. 1998). The models used in the RMA report employed RMP copper data to project values in the San Francisco Bay at both higher-high tide and at lower-low tide. The RMA report concluded that: "There may be large short-term variations in the concentration of total copper through the deposition and re-suspension processes. Observed variation in the concentration of dissolved copper are much less dramatic." Concentrations of copper observed in the current study and the City’s 1996-97 WER study verify these conclusions and should add greater precision to a water quality model of the South Bay, given the quantity of data collected. Further analysis of tidal differences with the City’s present study data will be useful in TMDL development.

Similar concentrations of total and dissolved copper were obtained in the City’s WER study (City of San Jose 1996/97) and the mean RMP data from years 1993 to 1996 (Figures 3 & 4.) Also, concentrations of the metal in the SJ/SC WPCP final effluent are shown for comparison. Most values are in very close agreement between the three studies. Symbols on the concentration bars indicate comparable stations between the studies. Mean dissolved copper agrees well when comparing stations, with a range of concentrations in the South Bay of 2.3 to 3.6 m g/L. Wide variability in the standard error bars of the two creek stations, SB11 and SB12, is likely due to the sporadic nature of stream flow, sediment load, pH fluctuations, and non-point sources of metals.

Mean total nickel was also highest in the creeks, decreasing at channel stations progressing northward in the South Bay (Figure 5). Concentrations of total nickel average approximately 31 and 28 m g/L in Coyote and Guadalupe Creeks, respectively. Most levels of total nickel in the South Bay ranged from 8 to 11 m g/L, with stations SB04 and SB05 showing the transition from non-point source input. The Water Quality Criterion for nickel in marine water is 8.3 m g/L. By contrast, mean total nickel in the final effluent was approximately 7.4 m g/L. This concentration was below any other mean total Ni value in the South Bay.

Mean dissolved nickel showed a very similar pattern to mean dissolved copper. Concentrations in Coyote Creek at Standish Dam (SB11) averaged 5.01 m g/L, and decreased further downstream. Stations SB04, SB05, and SB03 had mean dissolved nickel concentrations of 4.65, 3.65, and 3.43m g/L, respectively. In contrast, the mean dissolved nickel in the SJ/SC WPCP final effluent was 7.09 m g/L. Dissolved nickel constitutes 96% of the nickel discharged from the treatment plant. Some of the lowest percent dissolved-to-total nickel ratios were also observed just downstream of the confluence with Artesian Slough, as were observed for dissolved-to-total copper.

Inter-study comparisons of total and dissolved nickel with the City’s WER study and the mean RMP 1993 to 1996 data are presented in Figures 6 & 7. Also, concentrations of nickel in the SJ/SC WPCP final effluent are shown for comparison to the receiving water. Both mean dissolved and total nickel show similar relationships as did the mean dissolved and total copper. The station at the mouth of Coyote Creek (SB03, BA10, CC) showed agreement within a few tenths of a part per billion between the three studies for both dissolved and total nickel. Some differences between the studies may be explained by differences in tides. The City of San Jose’s WER study collected water only at high tide, whereas the current City study specifically collected samples from all tidal cycles. The RMP collects water samples from various tidal cycles. Standard error bars were large for total nickel at the two creek stations. Standard errors bars were proportionally less for dissolved nickel than for dissolved copper. Most mean dissolved nickel concentrations in the South Bay ranged from 2.4 to 5.0 m g/L. The RMP data showed a mean dissolved value of 7.4 m g/L Ni at station C-3-0, closest to Artesian Slough. This higher value may reflect dissolved nickel coming from the SJ/SC WPCP if most of the RMP samples were collected on ebbing or low tides. All of the mean dissolved nickel values for South Bay stations were below the Water Quality Criterion for nickel in marine water of 8.3 m g/L despite many mean total nickel concentrations exceeding that level.

Despite the fact a large proportion of nickel and copper discharged by the San Jose/Santa Clara Water Pollution Control Plant is predominantly dissolved metal, the observed impact to dissolved metals in the receiving water was not obvious. A dilution study performed in 1990 (CH2M HILL. 1990) concluded under worst case scenarios (dry season with little dilution of the effluent, neap tides, and Delta outflow at a minimum) that the dilution at SB04 (RMP site C-3-0) was 10.6. By the time the water reaches Calaveras Point (site SB03 and RMP site BA10) and northward, the dilution study concluded there would be dilution of >50/1.

Mean total selenium concentrations most dramatically demonstrated the influence of non-point source pollution (Figure 8). The mean total selenium concentration in Guadalupe Creek was 2.74 m g/L and 1.21m g/L in Coyote Creek at Standish Dam. Mean total selenium concentrations decreased northward in the South Bay with most values between 0.3 and 0.5 m g/L. Mean total selenium in the SJ/SC WPCP final effluent was 0.56 m g/L.

There was little difference in the dissolved and total selenium concentrations; thus the percent dissolved-to-total ratios reflect this fact. Mean percent dissolved selenium at most stations was over 80%. The percent dissolved selenium downstream of the confluence of Artesian Slough and Coyote Creek was similar to the percent dissolved selenium at Standish Dam (SB11). Dissolved selenium was not measured in the final effluent of the treatment plant.

An inter-study comparison of mean total mercury between the present study and mean RMP 1993 to 1996 data shows very good agreement and indicates that the sources of mercury may be upstream of the two creek stations (Figure 9). There are a number of abandoned cinnabar mines in the watershed of the two creeks draining into the South Bay. Stations SB04 and SB05 are among the highest of the South Bay stations with mean total mercury concentrations over 0.05 m g/L. Mean total mercury concentrations at other South Bay stations do not exceed the Water Quality Criterion of 0.025 m g/L.

Other water quality parameters (S%, TSS, and TOC) are shown in Figure 10. Mean salinity values were around 2% at the creek stations. Salinity increased along channel stations into the estuary, reaching a mean salinity of 22.2% at station SB01, north of Dumbarton Bridge. These measurements were taken at approximately one meter and do not characterize the tidal wedge of saline water that may be present along the bottom of the creeks and the South Bay at high tide. Total Suspended Solids were highest at stations SB03 and SB05, as were Total Organic Carbon values. These stations are geographically located in an area of the South Bay and creek system that provides an area of deposition for fine sediments. Silt and clay brought in by run-off and re-suspended particles transported off mudflats by the strong northwesterly winds in late Spring and Summer likely deposit at the south end of the Bay.

Mean concentrations of fecal coliform bacteria at the 12 study sites and in the SJ/SC WPCP final effluent are presented in Figure 11. Similar to metals, the source of bacteria was shown to be in the creeks draining into the South Bay. A mean fecal coliform value of 1300 MPN/100 ml was observed at Standish Dam (SB11) and just under 1000 MPN/100 ml observed on Guadalupe Creek (SB12). Concentrations of fecal bacteria decreased progressively northward into the Bay. Standard error bars were high at the creek stations and two stations in lower Coyote Creek (SB04 & SB05), likely reflecting the seasonal habits of birds and mammals that frequent these waterways. Levels of fecal bacteria and standard error bars were less pronounced in the South Bay away from sources of in-put, perhaps reflecting poor survival in a saline environment.

Since more than half of the South Bay consists of tidal mudflats and a large tidal prism cycles over shallow shoals, water quality is likely to vary depending on the tidal influences. Future statistical analyses will compare trace pollutant concentrations and water quality parameters at different tide cycles.

The current study serves as a valuable link between point source pollutant monitoring, watershed monitoring, and the Regional Monitoring Program. Increased spatial and temporal frequency of sampling in this study will likely provide greater confidence in modeling trace pollutant concentrations and loading in the South San Francisco Bay. Mean total metal concentrations were higher with greater variability than dissolved mean metal concentrations. Mean total and dissolved metals (copper, nickel, and selenium) decreased progressively from the two creek sites northward into the estuary. Percent dissolved-to-total copper and nickel ratios showed a noticeable decrease at the two stations in Coyote Creek downstream of the confluence with Artesian Slough. Concentrations of mean total and mean dissolved copper and nickel downstream of the SJ/SC WPCP were not significantly higher than metal concentrations in the ambient (up-stream) receiving water.

Total copper and nickel concentration frequently exceeded marine Water Quality Criteria values in the South Bay, whereas the mean dissolved levels of these two metals did not exceed the Criteria. Mean total mercury concentrations were highest at the two creeks and diminished to 0.025 m g/L (the marine Water Quality Criterion) or less in the South Bay. Inter-study comparisons of mean total and dissolved metals show good agreement of data with two previous studies. The current study links most pollutant concentrations, including fecal bacteria and mercury, in the South San Francisco Bay to the two major creeks, Guadalupe and Coyote Creeks, draining the watershed.