The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 1 

## Suisun Bay San Pablo Bay

Central Bay

South Bay

Figure 1. San Francisco Bay consists of four interconnected embayments. For indicator analysis, each embayment was considered as a subregion of the Bay. 

# San Francisco Bay Water Quality Index

INDICATOR ANALYSIS AND EVALUATION

A. Background

San Francisco Bay is a large dynamic estuary, connected to large rivers and small ephemeral streams, urban and agricultural watersheds, and the Pacific Ocean. The Bay is also an unusual "inland" estuary, consisting of four interconnected embayments or subregions, each of which differs with respect to the
amounts and sources of freshwater inflow, and the levels of urbanization along its shores (Figure 1). Water quality in the Bay, and its effects on the animals and plants that live in the estuary and people who enjoy those resources, is strongly influenced by inputs from
each of these connections.

Assessing and monitoring water quality in such a large and complex ecosystem is challenging. Transport of many contaminants into the Bay coincides with periods of high freshwater inflow, episodic and
often short-duration events in California's Mediterranean climate (see Freshwater Infow Index). Dispersal of contaminants within the Bay is driven by multiple freshwater inflows, strong tidal influences, and the complicated topography of the Bay. The list of contaminants detected in Bay waters continues to grow: new chemicals replace those found to be too harmful to use while older chemicals, discharged into the Bay or its tributaries years ago, still seep into Bay waters. Water quality standards, identifying contaminant concentrations that are harmful to aquatic life or human health, have been established for a number of contaminants found in the Bay but, for many chemicals, no guidelines exist.The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 2 

### B. Indicators

The Water Quality Index measures the levels of contamination of San Francisco Bay waters for several classes of toxic compounds and other adverse water quality conditions that are harmful to aquatic life and impair ecosystem function. The Index has five indicators, each based on a class of contaminants or water quality conditions:

1. Trace elements – Trace elements include elements, such as arsenic, and metals, including mercury and copper. Typically these contaminants enter Bay waters during high flow events or are re-suspended from Bay sediments. For many aquatic organisms, exposure to high levels of dissolved metals or other trace elements can be lethal or adversely affect reproduction or early development. Toxicity of a number of these contaminants is dependent on other water quality characteristics, primarily hardness (concentration of calcium carbonate, CaCo 3 , mg/L); for example, toxic effects of some dissolved metals are reduced in hard water compared to soft water. In addition, for the protection of aquatic life, different water quality standards may apply for fresh and salt waters. A number of trace elements, principally mercury and selenium, bioaccumulate in aquatic organisms in the Bay's food web.

2. Pesticides – Pesticides, herbicides and fungicides used throughout the San Francisco Bay Area and its upstream watersheds enter Bay waters as runoff and their concentrations in Bay waters often peak following rainfall events. These compounds, which are intended to control terrestrial pests, can be equally harmful or lethal to aquatic organisms.

3. PCBs – Polychlorinated biphenyls (PCBs) are a class of man-made chemicals developed in the 1920s and used extensively in a variety of industrial applications. By the 1970s, the health risks associated with PCBs were identified and publicized and, following direction by the U.S. Congress in 1976, the US EPA banned the manufacture of these compounds in 1978. PCBs are resistant to degradation and persist for many years in the environment. In addition, PCBs bioaccumulate in the food web and are stored in the body fat of animals and humans.

4. PAHs 

### – Polycyclic aromatic hydrocarbons (PAHs) are a group of chemicals that occur naturally in coal, crude oil, and gasoline. Most PAHs enter the environment from incomplete burning of oil, wood, garbage or coal, where they can persist for months of years. Identified health effects of PAH exposure include cancer and adverse reproductive and developmental effects. Present water quality standards for PAHs are for the protection of human health based on consumption of exposed aquatic organisms.

5. Dissolved oxygen – Low dissolved oxygen concentrations can kill fish and invertebrates and exclude many aquatic animals from large areas of habitat. Oxygen depletion usually results from high rates of microbial and/or algal respiration that exceed the capacity of the water body to replenish oxygen through phytoplankton photosynthesis and diffusion from the air. Excessive input s of organic material and nutrients, forThe Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 3 Figure 2. Regional Monitoring Program water sampling station in San Francisco Bay. example from poorly treated sewage discharges or surface runoff, can accelerate respiration rates and trigger localized and regional oxygen depletion.

Individual contaminants in each of the indicators are shown in Table 1.

Sediment Contamination – Pollutants are not only present in the Bay's open waters but are also found in the sediments on the Bay's bottom, particularly near the mouths of tributary streams. Contaminant-laden sediments are reintroduced to the Bay's open waters when shipping channels or other areas are dredged; as a result of tidal action; and/or during peak rainfall events. Thus, sediments can be a source of continued contamination to Bay waters as well being directly toxic to benthic (bottom-dwelling) organisms. Sublethal contamination of bent hic organisms is also an important pathway for bioaccumulation and biomagnification of contaminants in the food web. Future versions of the San Francisco Bay Water Quality Index will include an indicator for sediment quality to assess the condition of Bay sediments and changes in contamination levels through time.



### C. Methods and Calculations

1. Data sources

The Indicators were calculated for each year using data from the San Francisco Estuary Regional Monitoring Program for Trace Substances (RMP) 1 , which has conducted two or three surveys per year since 1993, sampling 26 stations distributed throughout Bay (Figure 2). Half of the stations are located in areas of the Bay that are predominantly salt water and half in
more estuarine areas with lower and
more variable salinities. Additional data for dissolved oxygen concentrations and for general evaluation of long-term trends in Bay water quality were obtained from the U. S. Geological Survey Ecology and Contaminants Project. 2

1 More information on the RMP can be obtained at www.sfei.org and at www.sfei.org/rmp/index/html

. RMP water quality data can be downloaded at www.sfei.o rg/rmp/data/rmpwater.htm.

2 More information on the USGS Ecology and Contaminants Project can be obtained at http://wwwrcamnl.wr.usgs.gov/tracel/ . Water quality data from this program are available for download at http://sfbay.wr.usgs.gov/access/wqdata.The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 4 2. Water Quality Standards

The concentrations of dissolved oxygen or contaminants assessed by each indicator were evaluated in relation to water quality standards established for the protection of aquatic life and human health by the U.S. Environmen tal Protection Agency (USEPA), California Toxics Rule (CTR), California Regional Water Quality Control Board (RWRCB), San Francisco Bay Region), and the California Depa rtment of Fish and Game (CDFG) (Table 1). 3 Water quality standards for the protection of aquatic life identify levels of contaminants that can be directly harmful to exposed plants and animals. Standards for the protection of human health are intended to prevent unacceptable accumulation of contaminants in aquatic organisms such that consumption of the organisms by human would be safe. Although the RMP monitors more than 120 contaminants, water quality standards have been established for only 41 chemicals and for dissolved oxygen. For a number of contaminants, concentrations deemed safe for the protection of aquatic life or human health differ between fresh water (defined as having salinity<5 ppt more than 75% of the time) and salt waters (salinity>5 ppt more than 75% of the time). For samples collected from the intermediate and variable salinity estuarine waters of the Bay, the most protective of the salt and fresh water standards was applied. For several dissolved metals with toxicities dependent on water hardness (concentration of calcium carbonate, CaCo 3 , in mg/L), the applicable standard was calcu lated based on hardness of the measured water sample.

3. Calculations

Each indicator was calculated using methods developed by the British Columbia Ministry of the Environment, Lands and Parks (Zandbergen and Hall, 1998) 4 and adopted by the
Canadian Council of Ministers of the Envi ronment (CCME, 2001). Using this method, calculation of each indicator incorporated three different measurements:

Scope ( how many? ) - the number of contaminants that exceeded water quality
standards

Frequency ( how often? ) - the proportion of samples for each contaminant that exceeded water quality standards

Amplitude ( how much? ) - the amount by which the samples exceeded water quality
standards

3 For more information on water quality standards used for the Water Quality Index see www.epa.gov/ost/standards/wqslibrary/ca/131.38.pdf

, www.swrcb.ca.gov/%7erwqcb2basinplan.htm , and www.sfei.org/rmp/index/html.

4 Zandbergen and Hall (1998) is availabl e at http://www.cciw.ca/33-4/33-4-519.htm.The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 5 Scope was calculated as: Scope = [(number of failed variables/total number of variables)]*100
where "failed variables" are the contaminants considered in the indicator that
exceeded the standard.

Frequency was calculated as: Frequency = [(number of failed tests)/(total number of tests)]*100 where "failed tests" are the samples tested for each contaminant considered in the
indicator that exceeded the standard.

Amplitude was calculated in three steps as:

a) Excursion i = [(failed test value i )/(objective i )]-1 where "i" is each sample test.

n b) NSE = 

## [ Σ excursion i )/(number of tests) 

## ]

i=1 where NSE is the normalized sum of the excursions.

c) Amplitude = {NSE/[(0.01(NSE) + 0.01]} where amplitude scales the NSE to a 100-point scale.

Each of these three measurements yielded results in a 100-point scale, with high values indicating greater contamination than low values.

The indicator 5 was calculated from the Scope, Frequency and Amplitude results as:

Indicator = 100 – {[sqrt(scope 2 + frequency 2 + amplitude 2 )]/1.732} where "sqrt" is the square root.

This final calculation also yielded results in a 100-point scale but, in contrast to its component metrics, high Indicator values corresponded to low levels of contamination (i.e., good water quality) and low values indicated high levels of contamination (i.e., poor water quality).

Calculations were conducted using a Microsoft Excel  macro, CCME Water Quality Index 1.0, available on request from the Canadian Council of Ministers of the
Environment. 6 For the PCBs and Dissolved oxygen indicators, data from stations in each of the Bay's four embayments, or subregions (i.e., South, Central, San Pablo, and Suisun

5 Although we use the result of this calculation as the "indicator", this value is referred to as the "CCME Water Quality Index" by the Canadian Council of Ministers of the Environment (CCME, 2001).

6 For further scientific information contact on the CCME Water Quality Index, see http://www..ec.gc.ca or contact Environmental Canada, Guidelines and Sta ndards Division, 351 St. Joseph Blvd., Hull, QC K1A 0h3, email: ceqg-rcqe@ec.gc.ca.The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 6 Bays), were partitioned and contaminants in each region were treated individually. Therefore, for these indicators, the "Scope" calculation yielded information on the number of subregions in the Bay in which the water quality standard was exceeded. For reference and validation of the collective Indicator results, expressed as the Water Quality Index, an additional calculation using the CCME Water Quality Index 1.0 Excel calculator was made using the data from all contaminant categories and all subregions (see F. Alternative Calculation of the Water Quality Index).The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 7 Table 1. Water quality standards for the protection and aquatic life and/or human health used for calculation of Water Quality Indicators. RWRCB=Regional Water Resources Control Board, San Francisco Basin Plan; USEPA=U.S. Environmental Protection Agency; CTR=California Toxics Rule; CDFG=California Department of Fish and Game.
Contaminant Standard Source Comments

Dissolved oxygen (mg/L) >5.0 mg/L RWRCB
Trace elements *

Ag (silver)** As (arsenic) Cd (cadmium)** Cr VI (chromium VI) Cu (copper)** Hg (mercury) Ni (nickel)** Pb (lead)** Se (selenium) Zn (zinc)** <1.9 ug/L <36 ug/L <2.2-9.3 ug/L <11-50 ug/L

<3.1 ug/L <0.012-0.025 ug/L <8 ug/L <2.5-8.1 ug/L

<5-71 ug/L

<81 ug/L USEPA * Fresh water and salt water
standards differ and the lower
of the two standards was
used for estuarine water samples. ** Ag, Cd, Cu, Ni, Pb, and Zn toxicities are dependent on water hardness, therefore
standards were calculated
based on hardness in the measured water sample.
Pesticides

Alpha-HCH
Beta-HCH Chlorpyrifos
Diazinon*
Dieldrin
Endosulfan I
Endosulfan II
Endosulfan sulfate
Endrin
Gamma-HCH Heptachlor Heptachlor oxide
Hexachlorobenzene
Mirex

p,p ∧ -DDD

p,p ∧ -DDE

p,p ∧ -DDT <13000 pg/L <46000 pg/L <5600 pg/L <40000 pg/L

<140 pg/L <8700 pg?l <8700 pg/L <240000000 pg/L <2300 pg/L <63000 pg/L

<210 pg/L <110 pg/L <770 pg/L <1000 pg/L <840 pg/L <590 pg/L <590 pg/L USEPA, CTR, and

CDFG * Water quality standard for diazinon for the protection of aquatic life developed by California Department of Fish and Game (Menconi and Cox, 1994).

PCBs (total, pg/L) <170 pg/L USEPA
and CTR
PAHs Acenaphthene
Anthracene Benz(a)athracene Benzo(a)pyrene Benzo(b)fluoranthene Benzo(k)fluoranthene Chrysene Dibenz(a,h)anthracene
Fluorathene
Fluorene Indeno(1,2,3-cd)pyrene Pyrene <270000 ng/L <110000000 ng/L <49 ng/L <49 ng/L <49 ng/L <49 ng/L <48 ng/L <49 ng/L <370000 ng/L <14000000 ng/L <49 ng/L <11000000 ng/L USEPA, CTR, and
RWRCBThe Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 8 

### D. Evaluating Results and Grading

For each indicator, the grading scale followed the "ranking" scale recommended by the CCME (2001). That scale also used five categories or levels that corresponded to specific levels of water quality impairment (Table 2). The Water Quality Index was calculated as the "grade point average" of the component indicators, and was reported as

a Grade (i.e., A-F) and a Score (i.e., the grade point average is expanded to a 100 point scale using a multiplication factor of 25).

Table 2. Grading scale and rationale used for the all Water Quality Indicators.

Indicator

(100-point scale) Ecological condition Grade point Grade

95-100 Excellent: water quality is protected with virtual absence of threat or impairment; conditions very close to natural or pristine levels 4 A

80-94 Good: water quality is protected with only minor degree of threat or impairment; conditions rarely depart from natural or desirable levels 3 B

65-79 Fair: water quality is usually protected but occasionally threatened or impaired; conditions sometimes depart from natural or
desirable levels 2 C

45-64 Poor (marginal*): water quality is frequently threatened or impaired; conditions often depart from natural or desirable levels 1 D

0-44 Very poor (poor*): water quality is almost always threatened or impaired; conditions usually depart from natural or desirable levels 0 F

* The CCME identifies the two lower levels with the te rms "marginal" (for a grade of D) and "poor" (for a grade of F), rather than "poor" and "v ery poor" as is used for indicato rs in other Scorecard Indexes.The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 9

Figure 3. The Trace Elements Indicator measures the concentration of dissolved trace elements in Bay waters in relation to the water quality standards for the protection of aquatic life. The Indicator is calculated from three metrics. Scope measures the number of contaminants and regions of the Bay in which concentrations were were above the standards. Frequency measures the proportion of water samples in which standards were not met. Amplitude measures the magnitude of each exceedence, the amount by which the
measured concentration for a contaminant exceeded the standard. 0 25 50 75 100

0 25 50 75 100

1993 1995 1997 1999 2001

0 25 50 75 100

1993 1995 1997 1999 2001 0 20 40 60 80 100 Scope
how many?

Frequency

how often?

Amplitude
h ow much? 

## A

B
C

D

F Grade



## Trace Elements E. Results

Indicator 1. Trace elements

The RMP monitors 14 trace elements in the Bay. These contaminants occur in Bay waters in both particulate and dissolved forms, but water quality standards apply only to dissolved trace elements and have been established for only ten of the monitored elements. Toxicity of the several of the dissolved metals depends on other water quality conditions, principally hardness and salinity. Figure 3 shows the results of the Trace
elements indicator calculations.

Water quality standards for most toxic trace elements found in the Bay were met in most water samples collected at most stations in the Bay. From 1993-2001, an average of 10% (range: 2-18%) of all water samples exceeded the standard for one or more trace elements. In 2001, 10% of samples failed for at least one
contaminant.The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 10 Figure 4. Concentrations of mercury, Selenium, and copper in the four subregions of the San Francisco Bay from 1993-2001. Each point is the contaminant concentration measured at a single station during a survey. Each line is the linear regression of the contaminant concentrations over time from a subregion. Note that mercury and selenium graphs use a log scale
on the Y axis. 1994 1996 1998 2000 2002Copper (ug/L)

0 1 2 3 4 5 6

South Bay Central Bay San Pablo Bay Suisun Bay fresh and salt water: 3.1 ug/LSelenium (ug/L)

0.01 0.1

1 10Mercury (ug/L)

0.0001 0.001

0.01 fresh water: 0.012 ug/L salt water: 0.025 ug/L

no data 2000-2001

fresh water: 5 ug/L Copper, mercury, selenium, and
nickel concentrations exceeded water quality standards in some years (Figure 4). Water quality standards for copper were exceeded in all years. Mercury concentrations (measured for only 1993-1999) exceeded standards in 1994, 1997 and 1998.
Selenium concentration standards
were exceeded in each of the last five years of the survey. Nickel
standards were exceeded at least once in most years.

Trace element contamination
was most severe in South and San Pablo Bays. Water quality exceedences for the four problem trace elements occurred exclusively in South and San Pablo Bays (Figure 4). No
exceedences were measured in either Central or Suisun Bays.

Concentrations of most of the problem trace element contaminants are declining (Figure 4). Mercury concentrations in South and San Pablo Bays declined significantly from 1993 to 1999 (regression, p<0.001, both subregions). Copper concentrations declined in all regions except San Pablo Bay (p<0.01, all subregions except San Pablo). Selenium concentrations have declined in areas except South Bay (p<0.001, all subregions except South Bay). In South Bay, selenium concen trations increased significantly during the nine-year period (p<0.001).The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 11 Figure 5. The Pesticides Indicator measures the concentrations of pesticides in Bay waters in relation to the water quality standards for the protection of aquatic life. The Indicator is calculated from three metrics. Scope measures the number of contaminants and regions of the Bay in which concentrations were were above the standards. Frequency measures the proportion of water samples in which standards were not met. Amplitude measures the magnitude of each exceedence, the amount by which the
measured concentration for a contaminant exceeded the standard.

0 25 50 75 100

0 25 50 75 100

1993 1995 1997 1999 2001

0 25 50 75 100

1993 1995 1997 1999 2001 0 20 40 60 80 100 Scope
how many?

Frequency

how often?

Amplitude
h ow much? 

## A

B
C

D

F Grade



## Pesticides Indicator 2. Pesticides

The RMP monitors 29 pesticides or pesticide breakdown products in the Bay but water quality standards have been established for only 17 of these contaminants. Figure 5
shows the results of the Pesticides indicator calculations.

Water quality standards for most pesticides found in the Bay were met in most water samples collected at most stations in the Bay. From 1993-2001, an average of 31% of all water samples exceeded the standard for one or more pesticides. In 2001, only 17% of samples had pesticide concentrations greater than the water quality standard. The percentage of water samples containing pesticide concentrations in excess of water quality standards was substantially lower in 2000 and 2001 (mean: 14%), the last two years for which data were available, than in any year between 1993 and 1999 (mean: 36%). However, fewer water samples were collected in 2000 and 2001 (18 samples/year compared to an average of 45 samples/year).The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 12 10 100 1000 10000

1 10 100 1000Concentration (pg/L)

1

10 100 1000

1994 1996 1998 2000 2002

100 1000 10000 100000 p,p -DDE

Heptachlor epoxide

Dieldrin

Diazinon

South Bay Central Bay San Pablo Bay Suisun Bay

Figure 6. Concentrations of mercury, Selenium, and copper in the four subregions of the San Francisco Bay from 1993-2001. Each point is the contaminant concentration measured at a single station during a survey. Each line is the linear regression of the contaminant concentrations over time from a subregion. Note that mercury and selenium graphs use a log scale
on the Y axis. Concentrations of diazinon, dieldrin, heptachlor epoxide, or DDT compounds exceeded water quality standards in all years (Figure 6). Dieldrin and DDE (a compound related to DDT) exceeded water quality standards in all years.
Standards for Diazinon and Heptachlor epoxide were exceeded in most years.

Pesticide contamination was most severe in South, San Pablo Bays, and Suisun Bay. Most pesticide exceedences
occurred in South and San Pablo Bays (Figure 6). For most of the problem pesticides, the highest
contaminant concentrations occurred in South and Suisun Bays. Concentrations of heptachlor epoxide were significantly higher in Suisun Bay than all other subregions
while Diazinon concentrations werehighest in South Bay. (KruskalWallis, p<0.05, both tests). DDE concentrations were equally high in South, San Pablo and Suisun Bays.

Concentrations of most of the problem pesticides have not declined (Figure 6). Diazinon, Dieldrin and DDE concentration did not significantly change during the nineyear 1993-2001 period. In contrast, concentration of heptachlor epoxide declined significantly in all areas of the Bay (regression, p<0.05, all subregions).The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 13 Figure 7. The PCB Indicator measures the concentration of PCBs in Bay waters in relation to water quality standard for the chemical. The Indicator is calculated from three metrics. Scope measures in how many regions of the Bay PCB levels exceeded the standard. Frequency measures the proportion of water samples in which the standard was exceeded. Amplitude measures the magnitude of each exceedence, the amount by
which the measured PCB concentration exceeded the standard. 0 25 50 75 100

0 25 50 75 100

1993 1995 1997 1999 2001

0 25 50 75 100

1993 1995 1997 1999 2001 0 20 40 60 80 100 Scope
how many?

Frequency

how often?

Amplitude

how much? 

## A

B
C

D

F Grade



## PCBs Indicator 3. PCBs

The RMP has identified 56 different polychl orinated biphenyls in San Francisco Bay waters. However, water quality standards for protection of aquatic life and human health (based on consumption of aquatic organisms exposed to PCB in fresh and salt water) for these chemicals apply to the summed concentration of all isomers and congener compounds (U.S. EPA and CTR). Figure 7 shows the results of the PCBs indicator
calculations.

PCB concentrations in San Francisco Bay exceeded water quality standards in every year, in every subregion of the Bay, and at nearly every sampling station. From 1993-2001, most water samples exceeded the standard by more than three-fold, with a median PCB concentration of 471 ng/L (compared to the standard of 170 ng/L). In South Bay, all but one water sample collected over the nine-year period exceeded the standard, while in Suisun Bay nearly 35% of all samples were in compliance with the PCB standard. In 2001, PCB concentrations in San Francisco Bay exceeded water quality standards for the protection of human health by nearly three-fold.The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 14 1994 1996 1998 2000 2002PCBs (ng/L)

100 1000 10000

South Bay Central Bay San Pablo Bay Suisun Bay water quality

standard (31 ng/L)

Figure 8. PCB concentrations in the four subregions of the San Francisco Bay from 1993-2001. Each point is the PCB concentration measured at a single station during a survey. Each line is the linear regression of
the contaminant concentrations over time from a subregion. Note that the Y axis uses a log scale. PCBs concentrations were highest in South Bay, intermediate in San Pablo Bay, and lowest in Central and Suisun Bays. From 1993-2001, median PCB concentrations in South Bay, 1172 ng/L, were significantly higher than those measured in all other areas of the Bay (Kruskal-Wallis ANOVA, p<0.05) (Figure 8). San Pablo Bay PCB concentrations, 472 ng/L, were lower than South Bay but significantly higher than
levels measured in either Central or Suisun Bays.

PCB concentrations are declining in most areas in the Bay. In Central, San Pablo and Suisun Bays, PCB levels significantly
declined from 1993 to 2001 (regression, p<0.05, all tests) (Figure 8). South Bay PCB levels have not declined (regression, p>0.5).The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 15 Figure 9. The PAHs Indicator measures the concentration of polycyclic aromatic hydrocarbons in Bay waters in relation to the water quality standards for the protection of aquatic life and human health. The Indicator is calculated from three metrics. Scope measures the number of contaminants and regions of the Bay in which concentrations were were above the standards. Frequency measures the proportion of water samples in which standards were not met. Amplitude measures the magnitude of each exceedence, the amount by which the measured concentration
for a contaminant exceeded the standard. 0 25 50 75 100

0 25 50 75 100

1993 1995 1997 1999 2001

0 25 50 75 100

1993 1995 1997 1999 2001 0 20 40 60 80 100 Scope
how many?

Frequency

how often?

Amplitude
h ow much? 

## A

B
C

D

F Grade



## PAHs Indicator 4. PAHs

The RMP has identified 25 different polycyclic aromatic hydrocarbons in San Francisco Bay waters. However, water quality standards have been established for only 12 of these individual PAH compounds. Figure 9 shows the results of the PAHs indicator
calculations.

Concentrations of PAHs in Bay waters exceeded water quality standards in four of nine years. Water quality standards for at least one of the 12 PAH compounds for which standards have been established were exceeded in 1995, 1996, 1997 and 2001. In 2001, one water sample from the South Bay had concentrations of two PAH compounds, benzo(b)fluoranthene and benz(a)anthracene, that exceeded standards for those
chemicals.The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 16 Figure 10. Total PAH concentrations in four subregions of San Francisco Bay from 1993-2001. Each point is the total PCB concentration measured at a single station during a survey. Each line is the linear regression of the contaminant concentrations over time from a subregion. Note that the Y axis uses a log scale. 1994 1996 1998 2000 2002Total PAHs (ng/L)

1 10 100 1000

South Bay Central Bay San Pablo Bay Suisun Bay South and San Pablo Bays had the highest levels of PAH pollution (Figure 10).
Total PAH concentrations were highest in South Bay, intermediate in San Pablo Bay lowest in Central and Suisun Bays (Kruskal-Wallis, p<0.05, all tests).

PAH concentrations in Bay waters did not change during the nine-year survey period (regression, p>0.1, all tests) (Figure 10).The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 17 Figure 11. The Dissolved Oxygen Indicator measures the concentration of dissolved oxygen in Bay waters in relation to the water quality standard for the protection of aquatic life. The Indicator is calculated from three metrics. Scope measures the number of regions of the Bay in which dissolved oxygen levels fell below the standard. Frequency measures the proportion of water samples in which the standard was not met. Amplitude measures the magnitude of each exceedence, the amount by which the measured dissolved oxygen concentration was below the standard. 0 25 50 75 100

0 25 50 75 100

1993 1995 1997 1999 2001

0 25 50 75 100



### 1993 1995 1997 1999 2001 0 20 40 60 80 100 Scope
how many?

Frequency

how often?

Amplitude
h ow much? 

## A

B
C

D

F Grade



## Dissolved Oxygen 5. Dissolved oxygen

Current water quality standards for dissolved oxygen in Bay waters require a minimum of 5 mg/L of dissolved oxygen. However, availability of oxygen for aquatic animals is more closely related to the % saturation of oxygen in the water, which is a function of water temperature and salinity as well as dissolved oxygen concentration. Oxygen saturation levels below 60-80% can be harmful to many aquatic animals and, in cooler and fresher Bay waters, oxygen concentrations above the minimum standard of 5 mg/L may be still be inadequate for the protection of aquatic life. Figure 11 shows the results of the Dissolved oxygen indicator calculations.

Dissolved oxygen concentrations were above the minimum standard in all areas of the Bay except the South Bay. In several years from 1993 and 2001, dissolved oxygen concentrations fell below the standard at the San Jose, Sunnyvale and Coyote Creek stations near the southern end of South Bay. In 2001, one water sample, collected at San Jose, failed to meet the minimum standard for dissolved oxygen.The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 18 Figure 13. Dissolved oxygen concentration measured at South Bay sampling stations by the RMP and the USGS Ecology and Contaminants Program. 2 4 6 8 10 12 14

1972 1976 1980 1995 2000Dissolved oxygen (mg/L)

2

4 6 8 10 12 14 Regional Monitoring Program (South Bay, 1993-2001)

USGS Ecology and Contaminants Project (South Bay, 1971-1978, 1993-2001) water quality standard (5 mg/L) 1994 1996 1998 2000 2002Dissolved oxygen (mg/L)

2 4 6 8 10 12 14

South Bay Central Bay San Pablo Bay Suisun Bay water quality

standard (31 ng/L)

Figure 12. Dissolved oxygen concentration measured in the in four subregions of San Francisco Bay from 1993- 2001. Each point is the dissolved oxygen concentration measured at a single station during a survey. Dissolved oxygen concentrations in South Bay were lower than
levels measured in other subregions of the Bay. South Bay oxygen concentrations were consistently and significantly
lower than those measured in allother regions of the Bay (KruskalWallis, p<0.05 all tests) (Figure 12). Oxygen concentrations were highest in Suisun Bay and, from 1993-2001, only one sample, collected in 1998, failed to meet the higher dissolved oxygen standard (7 mg/L) set by the RWQCB for Bay-Delta waters west
of Antioch.

Dissolved oxygen levels varied seasonally. Throughout the Bay, higher oxygen concentrations were measured during the spring, the result of high rates of photosynthesis dur ing the spring phytoplankton bloom (see Food Web Index) (Figures 12 and 13). Low dissolved oxygen conditions usually occurred during the summer months.

From 1993-2001, overall dissolved oxygen conditions in the Bay have not changed. However, based on the longer data record from the USGS Ecology and Contaminants Project, dissolved oxygen conditions in the South Bay have improved during the past thirty years (Figure 13). The USGS program, which samples more frequently and at stations that are farther from shore, measured consistently low dissolved oxygen in the South Bay throughout the 1970s (including one year in which oxygen
concentrations fell to zero following a uncontrolled release of inadequately treated sewage into the Bay, not shown in Fig 13, but see SFEI, 2003). Since 1993, the USGS program has not reported any samples with oxygen concentration
below the minimum standard.The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 19 1993 1995 1997 1999 2001 0 25 50 75 100 Grade Score

A

B

C

D

F

Figure 14. The Water Quality Index aggregates the results of the Trace elements, Pesticides, PCBs, PAHs, and Dissolved oxygen indicators.

Figure 15. Comparison of San Francisco Bay Water Quality Index calculated using the CCME Water Quality Index and all Bay contaminants (upper panel) and the Index calculated as the grade point average of the five Indictors (lower panel). 1994 1996 1998 2000 2002Water Quality Index(value calculated from three metrics)

40 60 80 100

1994 1996 1998 2000 2002Water Quality Index Score(expanded grade point average)

0 20 40 60 80 100 CCME Rank

Grade Excellent

Good

Fair

Marginal

Poor

(excellent)

(good)

(fair)

(very poor)

(very poor) A

B

C

D

F 6. Water Quality Index

The San Francisco Bay Water Quality Index aggregates the results of the Trace elements, Pesticides, PCBs, PAHs, and Dissolved oxygen indicators (Figure 14).

Between 1993 and 2001, water quality in the open waters of the Bay was fair (Grade = C) to good (Grade = B). Although the Water Quality Index has fluctuated slightly from year to year, it has not significantly increased or decreased duri ng the nine-year period for which indicator data were available (regression, p>0.05).



### F. Alternative Calculation of the Water Quality Index

In the above analysis, the Water Quality Index was calculated from separate analyses of several classes of contaminants, each class equally weighted despite different numbers
of constituent contaminants. An alternative approach to calculate
the Index uses the CCME Water Quality Index calculator for all of
the contaminants monitored in the Bay, a method that weights each individual contaminant equally. Figure 15 shows the Water Quality Index calculated using this alternative method and compares it with the Water Quality Index calculated as the grade point average of the five Indicators. Both approaches yielded similar results: San Francisco Bay water quality from 1993-2001 was generally fair to good and the small year-to-year variations in pollution
levels were consistent between the
two calculation methods.The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 20 Figure 16. Ammonia nitrogen and copper concentrations in wastewater effluent discharged into South Bay. Redrawn from U. S. Geological Survey, “San Francisco Bay Program: Lessons learned for managing coastal water resources”, http://water.usgs/wid/html/sfb/html.Ammonia nitrogen (mg/L)

0 5 10 15 20 25 30

1970 1975 1980 1985 1990 1995Copper (ug/L)

0 30 60 90 120 150 Ammonia nitrogen

CopperConcentration 

### G. Long-term Trends in Bay Water Quality

Although the earliest data from the San Francisco Estuary Regional Monitoring Program for Trace Substances (RMP) are from 1993, the U. S. Geological Survey has been conducting both monitoring and focused special studies on Bay water quality since the 1970s. Because the USGS monitoring studies are less comprehensive than the RMP with respect to the diversity of contaminants, the Water Quality Index indicators were calculated using only the RMP data. However, the USGS results were used to evaluate long-term trends in Bay water quality for selected contaminants.

Concentrations of ammonia nitrogen and copper declined substantially during the late 1970s and early 1980s (Figure 16). Following implementation of advanced wastewater treatment,
concentrations of ammonia nitrogen and copper in effluents discharged into South Bay declined substantially. Excessive nitrogen inputs can promote bacterial and algal blooms that can result in periodic and localized dissolved oxygen depletion. Since the 1970s,
incidences of low dissolved oxygen in the South Bay have also been reduced (see Dissolved oxygen indicator and Fig. 13).The Bay Institute Ecological Scorecard San Francisco Bay Water Qu ality Index October 17, 2003 Page 21 

### H. References

CCME (2001) Canadian water quality guidelines for the protection of aquatic life. CCME Water Quality Index 1.0 User's Manual. In: Canadian environmental quality guidelines, 1999, Canadian Council of Ministers for the Environment, Winnipeg.

Cloern, J. E., S. N. Luoma, and F. H. Ni chols (1995) San Francisco Bay Program: lessons learned for managing coastal water resources. U.S. Department of Interior, U. S. Geological Survey, Fact Sheet FS-053-95. This article is available at http://water.usgs.gov/wid/html/sfb.html.

Menconi, M. and C. Cox (1994) Hazard assessment of the insecticide diazinon to aquatic organisms in the Sacramento-San Joaquin river system. Administrative Report 94-2. California Department of Fish and Game. Rancho Cordova, CA.

San Francisco Estuary Institute (SFEI) (2003) The Pulse of the Estuary: Monitoring and Managing Contaminants in the San Francisco Estuary. SFEI Contribution 74. San Francisco Estuary Institute, Oakland, CA.

Zandbergen, P. A. and K. J. Hall (1998) Analysis of the British Columbia Water Quality Index for watershed managers: a case study of two small watersheds. Water Qual. Res. J.
Canada 33: 519-549. This article is available at http://www.cciw.ca/33-4/33-4-519.htm.