Document Details

San Francisco Bay: A Freshwater Starved Estuary

The Bay Institute (Bay Institute) | September 1st, 2016

How Reducing Flows Harms the Ecosystems of San Francisco Bay and Coastal Waters

The Bay Institute’s major new study, San Francisco Bay: The Freshwater – Starved Estuary, documents how the ecological health of San Francisco Bay and the nearby ocean is at high risk because large-scale water diversion in the Bay’s watershed severely limits the amount of fresh water that reaches the Bay and alters the timing of that flow. Inflow to the Bay from its Central Valley watershed now averages less than half of what it would be without diversions; in some years just one-third of the runoff makes it to the Bay. The result is a nearly permanent drought for the Bay’s fish, wildlife, and their habitats. This radical alteration creates severe consequences for the Bay and marine ecosystems – and Bay Area residents pay the price.

The study shows how unsustainable diversion of the Bay’s freshwater inflow:

Dramatically cuts production of fish and shrimp that are the food source for marine mammals, like Orca Whales, and birds;

Allows pollutants to accumulate to dangerous levels and encourages blooms of toxic algae;

Reduces sediment supply to Bay Area wetlands and beaches;

Makes it easier for undesirable non-native species to successfully invade the Bay Estuary.

The San Francisco Bay Estuary is created by the mixing of fresh water from the Central Valley’s rivers with salt water from the Pacific Ocean. Dramatically reducing the inflow of fresh water generates cascading effects in the Bay’s watershed, the Bay itself, and coastal ocean waters.

The report’s major findings include:

On average, since 1975 more than half (53%) of runoff from the Central Valley watershed has been diverted, stored, or exported before it can reach the Bay – and in many years two-thirds or more of the Bay’s inflow is captured;

As a result of intensive water diversions, the Bay experiences catastrophically dry years almost half the time (only one “supercritically dry” year occurred naturally between 1975-2014, but the Bay experienced nineteen supercritical years during that period);

Numerous unrelated fish species – from sharks to salmon, from sturgeon to smelt – show strong positive correlations with Bay Inflow; many of these species are now endangered, and even commercially viable fisheries are in decline;

Predators that feed on flow-dependent fish and shrimp are feeling the pinch – for example, dwindling supplies of Central Valley Chinook salmon may restrict the recovery of the local Orca whale population;

Blooms of toxic “algae” (cyanobacteria) are becoming more frequent, and other pollutants are becoming more concentrated, as a result of reductions in freshwater flows from the Bay’s watershed;

Bay Area beaches and tidal wetlands are deprived of sediment that was once transported by high river flows.

The study reports that local businesses are likely to suffer from the Bay’s continued decline, including those related to commercial fishing and tourism. As our Bay, beaches, wetlands, and fish and wildlife populations deteriorate, the quality of life for many Bay Area residents will also be severely – and perhaps permanently – damaged.

The study identifies four important approaches to improving Bay inflows:

Update the State’s 21 year old water quality standards for the Bay Estuary to ensure adequate inflow

Require all those who divert water destined for the Bay, not just a subset, to contribute their fair share of fresh water to support benefits enjoyed by all Californians

Invest in local water supplies around the state including conservation, and recycling, that can generate millions of acre-feet of water and reduce reliance on water diverted from the Estuary and its watershed

Coordinate management of flows with wetland and beach restoration to more effectively protect shorelines

The study was prepared for the San Francisco Estuary Partnership, a coalition of resource agencies, non-profits, citizens, and scientists working to protect, restore, and enhance water quality and fish and wildlife habitat in and around the San Francisco Bay Delta Estuary, which also provided the majority of funding for the project.


adaptive management, ecosystem management, endangered species, salinity, water project operations, water quality, wetlands