Ecology of The San Francisco Estuary - Physical Geography

Physical Geography

The San Francisco Bay is both a bay and an estuary. The former term refers to any inlet or cove providing a physical refuge from the open ocean. An estuary is any physiographic feature where freshwater meets an ocean or sea. The northern portion of the Bay is a brackish estuary, consisting of a number of physical embayments which are dominated by both marine and fresh water fluxes. These geographic entities are, moving from saline to fresh (or west to east): San Pablo Bay, immediately north of the Central Bay; the Carquinez Strait, a narrow, deep channel leading to Suisun Bay; and the Delta of the Sacramento and San Joaquin Rivers.

Until the 20th Century, the LSZ of the Estuary was fringed by tule-dominated freshwater wetlands. Between 80-95% of these historic wetlands have been filled to facilitate land use and development around the Bay Area. Habitat loss at the edges of the pelagic zone is thought to create a loss of native pelagic fish species, by increasing vulnerability to predation.

The intertidal and benthic Estuary is presently dominated by mudflats that are largely the result of sedimentation derived from gold mining in the Sierras in the late 19th Century. The trend toward high sediment loads was reversed in the 1950s with the advent of the Central Valley Project, locking up most sediment behind dams, and resulting in an annual net loss of sediments from the Estuary. Thus the mudflats appear to be slowly receding, although turbidity remains extremely high. The high turbidity of the water is responsible for the unique condition that exists in the San Francisco Estuary wherein high nutrient availability does not lead to high phytoplankton production. Instead, most algae photosynthetic organisms are light-limited.

The Delta has likewise experienced heavy alteration. Beginning in the 19th Century, naturally occurring levees were reinforced for permanency, to protect farmlands from regular flooding. Many of these farms were established on peat islands occurring in the middle of the Delta waterways. Intensive farming oxidized the high carbon content of the soil, causing considerable loss of soil mass. As a consequence, these islands have subsided, or sunk, to nearly 6 meters below sea level. The Delta today consists of highly riprapped waterways, punctuated by islands that appear like "floating bowls" with their basins far below the surface of the water. These islands are at high risk for flooding due to levee collapse. The subsequent eastward shift in salinity is expected to dramatically alter the ecology of the entire LSZ of the San Francisco Estuary.