Subtidal Habitat

Mark Herzog, Josh Ackerman, Susan W. De La Cruz (U.S. Geological Survey);
Jill Demers (San Francisco Bay Bird Observatory); Cheryl Strong (U.S. Fish and Wildlife Service)

Status: Most diving and sea duck species are stable, but four species are declining.

Subtidal habitat is the habitat below the surface of San Francisco Bay, typically submerged. Birds using the subtidal habitat in the bay feed on fish, shellfish (including mussels), invertebrates, underwater plants, and algae.

Sea Ducks (blue) – Overall stable but may be declining in the past two decades. Diving Ducks (red) – Populations are variable with no clear trend.


Greater Scaup

Greater Scaup

Surf Scoter

The species of sea and diving ducks wintering in San Francisco Bay show stable populations, with the following exceptions:

Canvasback (a diving duck): Nationally, Canvasback numbers are highly variable around a long-term average of about 600,000. Locally, their wintering numbers in the Bay have shown long-term decline, perhaps due to habitat loss in the Bay or the creation of habitat in areas like the Central Valley.

Scaup (a diving duck) and scoters (sea ducks) are declining throughout North America as well as in the Bay. The San Francisco Bay populations of these two groups of ducks represent, on average, between 40% and 50% of all scaup and scoters counted in the Pacific Flyway. If conditions change in San Francisco Bay, a large percentage of the population may be affected.


Primary threat: Reduced quality and quantity of wintering habitat from increasing contaminants (selenium, cadmium, and mercury); loss of deep pond habitat; and changes in prey species composition.

Climate change and sea level rise, resulting in changed salinities and water depth. This could alter prey composition and herring spawning.

Loss of herring stock in San Francisco Bay and along the Pacific Coast. Herring spawn is important in diving duck diets, particularly for scoters during spring migration, but also is used heavily by scoters and scaup throughout the winter.

Disturbance from boat traffic flushes groups of resting or foraging ducks off the surface of the water.

Winter oil spills have the potential for catastrophic impact to duck populations.

Declining availability of quality breeding habitat in Alaska, Canada, and the northern Intermountain West Region.


Planning, Management, Restoration

Ensure that wintering habitat remains available for sea ducks and diving ducks, by restoring and preserving deeper and less saline water ponds within restoration areas such as South San Francisco Bay and Napa-Sonoma Marsh.

Minimize pollution from runoff by working with local governments and communities to create programs that reduce runoff (e.g. reducing impervious surfaces) and upgrade storm water and sewage treatment plant facilities.

Reduce contaminant release when conducting restoration activities by maintaining deeper water depths. Special care should be taken to minimize actions that increase contaminant release (mercury, selenium, and cadmium) or methylmercury production in shallow water areas.

Minimize disturbance in key foraging areas from recreational and ferry boats, especially in the following areas: in northern San Pablo Bay; near eelgrass beds; and within the central part of San Francisco Bay from the Bay Bridge to the San Mateo Bridge.

Encourage restoration of eelgrass, which is a substrate for herring spawn and prey species like crabs, mussels, and small fish.

Implement the Subtidal Habitat Goals Report recommendations for the restoration, protection, and science needed to protect this habitat type –


Continue the USFWS mid-winter waterfowl survey, which has provided a consistent record of winter waterfowl populations since 1955.

Assess contaminants through studies of mercury concentrations in nesting birds.

Study prey density and waterfowl feeding behavior to determine high-quality habitat that should be protected or enhanced (e.g. eelgrass, creek mouths, ponds, shoals).

Model carrying capacity of intertidal and subtidal habitats to help set wintering population goals. Current efforts have shown the value of San Pablo Bay subtidal habitats, and they point to prey distribution and fish and shorebird competitors as key elements in future modeling efforts that incorporate all sub-bays.

Evaluate the effects of human disturbance on foraging and roosting birds.

Model sea level rise, salinity, and sediment to help predict how benthic prey availability in subtidal and intertidal habitats may change in the future.

Determine habitat connectivity among San Francisco Bay, migratory corridors, and breeding areas to help establish flyway-wide conservation efforts year-round.