San Francisco Bay Program:
Lessons Learned for Managing Coastal Water Resources
The USGS provides maps, reports, and information to help
others meet their needs to manage, develop, and protect America's water,
energy, mineral, and land resources. We help find natural resources
needed to build tomorrow, and supply scientific understanding needed to
help minimize or mitigate the effects of natural hazards and environmental
damage caused by human activities. The results of our efforts touch the
daily lives of almost every American.
Index of Subjects:
- Nutrient Enrichment
- Toxic Contaminants
- Biological Contamination
Coastal ecosystems, such as bays and estuaries, are among our most
disturbed natural environments. These ecosystems also are among our most
valuable habitats--estuaries supported U.S. fisheries valued at $19 billion
in 1990. Although many human activities cause change in the coastal zone,
they occur against a background of natural change. Effective coastal-zone
management requires that we identify and understand these separate causes
of ecosystem change. With this goal in mind, the United States Geological
Survey (USGS) began in 1968 a broad program of scientific study in San
Francisco Bay (fig. 1). The program is based on a conviction that
sustained, multifaceted investigation of one estuary will produce general
lessons to guide the management of natural resources associated with all
(fig. 1) San Francisco Bay has been a focus of intensive investigation
by the USGS since 1968.
The USGS San Francisco Bay Program has produced more than 250 reports,
including three books and a review of the human modifications of the Bay.
These publications are a source of guidance to resource managers as they
work to understand how human activities (such as water diversion,
commercial trade, and waste inputs) cause change in the coastal zone. The
program has been organized around themes. One of the most important themes
is the integrated study of nutrients, toxic substances, and living
resources at lower levels of the food chain--the phytoplankton and bottom
dwelling invertebrates. Close collaboration between chemists and
ecologists has helped to explain how plant and animal species of coastal
ecosystems are organized into food chains, how nutrients and toxic
contaminants are incorporated into these food chains, and how the lessons
learned from detailed scientific understanding can be applied to develop
effective monitoring programs and rational environmental standards.
Human settlement around coastal water bodies has led to increased inputs
of nutrients such as nitrogen and phosphorus. Many estuaries are now among
the most intensively fertilized environments on Earth. Each day, San
Francisco Bay receives more than 800 million gallons of municipal
wastewater containing 60 tons of nitrogen.
Water-quality managers need to know how nutrient inputs cause changes in
water quality, the natural capacity of coastal waters to assimilate added
nutrients, the level of waste treatment required to protect living
resources from the harmful effects of nutrient enrichment, and if programs
of nutrient reduction are having beneficial effects.
Since 1968, the continuous study of San Francisco Bay by the USGS has
given that agency a unique opportunity to follow ecosystem responses to
improved wastewater-treatment methods as mandated by State and Federal
legislation. One result of the implementation of these improved methods
has been a large reduction in the input of ammonia-nitrogen from some
municipal wastewater-treatment facilities (fig. 2).
(fig. 2) Implementation of advanced wastewater treatment in 1979
immediately reduced the input of ammonia- nitrogen to South San Francisco
Bay. In prior decades, the South Bay had repeated episodes of oxygen
depletion and animal die-offs. USGS measurements have shown a complete
cessation of these episodes since 1980. Spawning salmon have recently been
observed in South Bay streams for the first time since the early 1900's.
See figure 1 for location of site.
USGS studies show that in spite of its nutrient enrichment, San Francisco
Bay has not been affected by harmful algal blooms. This seeming paradox is
explained partly by the abundant bottom-dwelling invertebrates (small
clams, mussels, crustaceans) that filter the water and remove new algae as
fast as they are produced. Feeding by these animals is a form of natural
waste treatment that helps control the growth of algae in a nutrient-rich
Concepts and measurement techniques from this USGS program are now
incorporated into a locally funded and managed Regional Monitoring
- The chemical quality of coastal waters can respond almost immediately
to waste-treatment improvements.
- Responses of biological communities to these chemical changes can take
years or even decades.
- Coastal water bodies have differing sensitivities to waste loading.
The most cost-effective national strategy for regulating nutrient inputs
will consider these differences among ecosystems.
Toxic contaminant inputs from industrial, agricultural, and commercial
activities are a high-priority concern in the changing Bay ecosystem. San
Francisco Bay receives effluents from 46 publicly owned
wastewater-treatment plants, 65 large industrial discharges, and as much
as 40,000 tons of at least 65 contaminants each year. Many of these
contaminants are toxic to plants or animals or pose threats to human
Water-quality managers expect from the scientific community reliable
answers to questions about the origins of toxic substances, how toxic
substances cause change in aquatic ecosystems, how these changes can be
remedied, and if the $70 billion national investment in
wastewater-treatment facilities is justified.
Comprehensive study of toxic trace metals by the USGS has shown that
contamination levels in San Francisco Bay accelerated during the 1950's.
Some Bay locations are among the most highly polluted coastal sites in the
United States. Contamination by silver, cadmium, lead, and selenium is
especially high. These metals are of particular concern because they can
impair the growth or reproduction of fish, birds, and mammals.
In response to these concerns, the USGS developed a biological monitoring
procedure that has been used continuously since 1977 near a
waste-treatment facility. Monitoring continued as wastewater-treatment
technologies improved. This is the longest continuous record of
contaminant concentrations in a natural environment of the United States
(fig. 3). The transfer of monitoring procedures developed by the USGS to
local agencies and businesses serves as a model of cooperation between
research and regulatory agencies.
(fig. 3) Steps of improved wastewater treatment have gradually reduced
the inputs of toxic metals to San Francisco Bay. USGS monitoring has shown
that these investments to remove contaminants have resulted in
improvements in some indicators of biological health, such as metal
concentrations in clams living near a wastewater discharge. See figure 1
for location of site.
In 1990, the USGS began a special series of investigations to describe the
origins and effects of toxic contaminants in San Francisco Bay. Early
results have shown that pesticides (such as diazinon) applied in the
Central Valley of California are carried by rivers into the Bay at levels
exceeding national guidelines. Biological tests have shown river waters to
contain high levels of pesticides soon after they are applied to fields.
The multifaceted USGS program has given local managers an objective
scientific basis for identifying the most critical contaminant issues, and
for establish-ing priorities. On the basis of high-quality data from the
USGS, Bay area inhabitants are now concerned with the effects of toxic
contaminants rather than nutrient enrichment.
- Public concern about the effects of toxic contaminants on coastal
organisms is justified. Trace metals and pesticides are periodically found
in San Francisco Bay at levels that can cause toxicity or impairment of
- Sustained biological monitoring indicates that reduced discharge of
toxic substances into coastal waters yields ecosystem benefits.
- Some ecosystem responses to reductions in contaminant loading are
gradual and continue for many years after the reductions have begun.
Management strategies for assessing the benefits of waste treatment need
to include long-term monitoring of results once actions are taken to
- The protection of coastal ecosystems requires a strategy for
prioritizing pollutant concerns followed by strategies for reducing inputs
on the basis of these priorities. Integrated assessments by teams of
chemists and biologists are effective for identifying and prioritizing
human activities that threaten the integrity of coastal ecosystems.
One unexpected result of commerce can be the movement of plants and
animals to new environments. Biological contamination by exotic species is
a particular problem in coastal environments where organisms are
redistributed by commercial shipping. More than 130 introduced species of
plants, invertebrates, and fish live in San Francisco Bay. Many of these
have displaced native species.
As regulators search for strategies to protect living resources, they ask
how habitat loss and biological contamination can change coastal
ecosystems, if these disturbances permanently change fish or bird
populations, how these changes compare to those caused by chemical
contamination, and if current regulation of biological contamination is
adequate or necessary.
Continuous long-term investigation of San Francisco Bay has given the USGS
a rare opportunity to measure ecosystem changes following invasion by a
highly successful exotic species. The Asiatic clam, Potamocorbula,
was introduced to the Bay in 1986, probably by a cargo ship. A cascading
sequence of ecological changes followed (fig. 4), similar to changes in
the Great Lakes after their invasion by the zebra mussel. These
fundamental ecological changes have likely contributed to the population
declines of almost every fish species living in the North Bay.
(fig. 4) USGS studies have documented the remarkable invasion of San
Francisco Bay by the Asiatic clam, Potamocorbula. Colonization by
this filter-feeding clam has led to depletions of phytoplankton in the
North Bay. Phytoplank-ton are a food source for small zooplankton animals
that, in turn, are a critical food resource for young fish. Zooplankton
abundance has dropped since the 1986 Potamocorbula invasion, and
most fish populations also have declined in the North Bay. See figure 1
for location of site.
- The complex ecological consequences of biological contamination can be
revealed only through consistent measurement programs that are sustained
before and after introductions of new species.
- Biological contamination can cause ecosystem changes just as powerful
as those caused by chemical contamination.
- Protection of living resources requires an ecosystem view that
considers the multiple effects of all sources of human disturbance,
including biological introductions.
from U.S. Department of the Interior, U.S. Geological
Survey, Fact Sheet FS-053-95
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Last modified: 1130 01 Apr 97 dlb