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Climate-Driven Ocean Changes Affect Estuaries

USGS scientist preparing a submersible instrument package into the San Francisco Bay, Calif.
USGS scientist preparing a submersible instrument package that is used to collect water-quality data on the San Francisco Bay, Calif., during a cruise of the USGS Research Vessel Polaris. The instrument includes sensors for measuring depth, conductivity, temperature, suspended solids, chlorophyll, light penetration, and dissolved oxygen.

Pacific Ocean Cooling Triggers Phytoplankton Blooms in San Francisco Bay

Long-term studies by U.S. Geological Survey (USGS) scientists have found that a cooling in ocean temperatures led to increased phytoplankton blooms and red tides in San Francisco Bay, California. The declining temperatures took place off the coast of California between 1999 and 2004.

This is a surprising result because scientists and water-resource managers normally associate phytoplankton blooms with increases in the amount of nutrients, such as nitrogen and phosphorus, entering estuaries from such sources as wastewater treatment plants and runoff from agricultural fields. In this case, the phytoplankton blooms in the Bay occurred during a period of decreasing nutrient concentrations and inputs.

The scientists discovered the effects of the cold Pacific temperatures by using water-quality and biological data collected over 25 years. The colder temperatures caused changes in the types, abundance, and migration patterns of marine life in the San Francisco Bay and costal ocean waters. The drop in temperature caused marine life, such as fish, shrimp, and crabs, to migrate to warmer waters, like San Francisco Bay.

The migrations caused an increase in the numbers of predators, such as Bay shrimp and Dungeness cabs, that eat filter feeders, such as clams. Clams can filter large quantities of phytoplankton from the Bay’s water, which can prevent phytoplankton blooms. With the increase in predators, there was a corresponding decrease in clam populations and an increase in the amount of phytoplankton.

A graphs summarize the data used to document the changes in San Francisco Bay phytoplankton
This set of graphs summarize the data used to document the changes in San Francisco Bay phytoplankton (as measured by chlorophyll a concentrations) caused by the decrease in ocean temperature.

Results of this study show that:

  • Changes in oceans, such as temperature, can cause corresponding changes in adjacent estuaries,
  • Nutrient enrichment is not the only cause of phytoplankton blooms in estuaries,
  • Estuarine restoration and protection programs could benefit from (1) a wider geographic perspective that recognizes the coastal ocean as an important source of estuarine variability, and (2) a longer time perspective that recognizes the importance of climate processes that fluctuate over periods of decades, and
  • Long-term collection of both physical and biological data are key to understanding and revealing the underlying causes of changes in biological communities and how ecosystems function.

Water-resource managers tasked with implementing programs to restore or protect estuaries can use these results to help develop more effective policies concerning phytoplankton blooms and nutrient enrichment in estuaries.


Cloern, J.E., Jassby, A.D., Thompson, J.K., and Hieb, K.A., 2007, A cold phase of the east pacific triggers new phytoplankton blooms in San Francisco Bay: Proceedings of the National Academy of Sciences of the United States of America, v. 104, no. 47, p. 18561-18565, doi:10.1073/pnas.0706151104.

Cloern, J.E., Jassby, A.D., Schraga, T.S., and Dallas, K.L., 2006, What is causing the phytoplankton increase in San Francisco Bay?, in The Pulse of the Estuary -- Monitoring and managing water quality in the San Francisco Estuary: San Francisco Estuary Institute Annual Report 2006, p. 62-70.

USGS scientists picking clams out of San Francisco Bay bottom sediments in box sieves on board the USGS Research Vessel Polaris
USGS scientists picking clams out of San Francisco Bay bottom sediments in box sieves on board the USGS Research Vessel Polaris.

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