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Phytoplankton Blooms in San Francisco Bay - Frequently Asked Questions

Q. - I thought phytoplankton blooms were bad. Why are they needed in San Francisco Bay?

A. - Phytoplankton are an important part of most aquatic food webs and are therefore important in aquatic ecosystems. As with land plants, these single-celled plants may grow faster during the increased light of spring or summer, resulting in a phytoplankton bloom. Larvae of many animals, including fish, shrimp, crabs and other invertebrates depend on this increased food production to feed their young. Thus, phytoplankton blooms are a natural phenomena in most aquatic systems, such as the San Francisco Bay. In most healthy aquatic systems phytoplankton blooms are limited in duration by the amount of nutrients available or by these grazers.

Q. - What makes the San Francisco Bay different from other estuaries that are plagued by phytoplankton blooms?

A. - In many estuaries that are surrounded by urban and agricultural areas, such as the Chesapeake Bay and San Francisco Bay, the level of nutrients can be artificially high due to run-off from suburban lawns and gardens, agricultural fields and other sources and due to wastewater discharges. This can result in rapid phytoplankton growth. Very large, poorly controlled phytoplankton blooms, such as those that occur in the Chesapeake Bay, can result in oxygen deficits in the bay’s water as the algae die. Although San Francisco Bay has high nutrient levels, it is also a very turbid system because there is lots of sediment in the water. The high turbidity limits the amount of light penetrating San Francisco Bay’s water. Therefore, the phytoplankton growth rate is limited by its ability to get sufficient light during most periods of the year and blooms are usually short lived and not very large.

More Information


Cloern, J.E., 2001, Our evolving conceptual model of the coastal eutrophication problem: Marine Ecology Progress Series, v. 210, p. 223-253.

Thompson, J.K., 2005, One estuary, one invasion, two responses--Phytoplankton and benthic community dynamics determine the effect of an estuarine invasive suspension-feeder, in Dame, R.F., and Olenin, S., eds., The comparative roles of suspension-feeders in ecosystems: the Netherlands, Springer Press, p. 291-316.

Lucas, L.V., Koseff, J.R., Cloern, J.E., Monismith, S.G., and Thompson, J.K., 1999, Processes governing phytoplankton blooms in estuaries—Part I, The local production-loss balance: Marine Ecology Progress Series, v. 187, p. 1-16.

Lucas, L.V., Koseff, J.R., Monismith, S.G., Cloern, J.E., and Thompson, J.K., 1999, Processes governing phytoplankton blooms in estuaries—Part II, The role of horizontal transport: Marine Ecology Progress Series, v. 187, p. 17-30.

Thompson, J.K., 1999, The effect of infaunal bivalve grazing on phytoplankton bloom development in South San Francisco Bay: Stanford, Calif., Stanford University, Department of Civil and Environmental Engineering, Ph.D. Thesis, 419 p.

Thompson, J.K., 2002, The evolving benthic community, in Science and Strategies for Restoration--San Francisco Bay Sacramento-San Joaquin River Delta Estuary: San Francisco Estuary Project and CALFED, p. 66-67.


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