The Bay Institute Ecological Scorecard San Francisco Bay Water Quality 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 Quality 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, CaCo3, 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 inputs of organic material and nutrients, for 
The Bay Institute Ecological Scorecard San Francisco Bay Water Quality 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 benthic 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.org/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 Quality 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. Environmental Protection Agency (USEPA), California 

Toxics Rule (CTR), California Regional Water Quality Control Board (RWRCB), San 

Francisco Bay Region), and the California Department 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, CaCo3, 

in mg/L), the applicable standard was calculated 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 Environment (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 available at http://www.cciw.ca/33-4/33-4-519.htm. 
The Bay Institute Ecological Scorecard San Francisco Bay Water Quality 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) Excursioni = [(failed test valuei)/(objectivei)]-1 

where "i" is each sample test. 

 n 

 b) NSE = [Σ excursioni)/(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 indicator5 was calculated from the Scope, Frequency and Amplitude results as: 

 Indicator = 100 – {[sqrt(scope2 + frequency2 + amplitude2)]/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 Standards Division, 351 St. Joseph Blvd., Hull, QC K1A 

0h3, email: ceqg-rcqe@ec.gc.ca. 
The Bay Institute Ecological Scorecard San Francisco Bay Water Quality 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 Quality 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 

RWRCB 
The Bay Institute Ecological Scorecard San Francisco Bay Water Quality 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 terms "marginal" (for a grade of D) and "poor" (for a 

grade of F), rather than "poor" and "very poor" as is used for indicators in other Scorecard Indexes. 
The Bay Institute Ecological Scorecard San Francisco Bay Water Quality 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

how 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 Quality 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 2002

Copper (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/L

Selenium (ug/L)

0.01

0.1

1

10

Mercury (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 concentrations increased significantly during the 

nine-year period (p<0.001). 
The Bay Institute Ecological Scorecard San Francisco Bay Water Quality 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

how 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 Quality Index 

October 17, 2003 Page 12 

10

100

1000

10000

1

10

100

1000

Concentration (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 were 

highest 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 Quality 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 polychlorinated 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 Quality Index 

October 17, 2003 Page 14 

1994 1996 1998 2000 2002

PCBs (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 Quality 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

how 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 Quality 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 2002

Total 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 Quality 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

how 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 Quality 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 2000

Dissolved 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 2002

Dissolved 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 all 

other 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 during 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 Quality Index 

October 17, 2003 Page 19 

1993 1995 1997 1999 2001

0

25

50

75

100

Score Grade

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 2002

Water Quality Index 

(value calculated from three metrics)

40

60

80

100

1994 1996 1998 2000 2002

Water 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 during 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 Quality 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 1995

Copper (ug/L)

0

30

60

90

120

150

Ammonia nitrogen

Copper

Concentration

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 Quality 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. Nichols (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.