Estuaries like San Francisco Bay are constantly changing, and they have complex patterns of water quality variability because they are mixing zones between the ocean and the land. Freshwater, sediments, nutrients, toxic contaminants, and other materials are carried to the estuary by river flow. River flow changes from season to season and year to year, so water quality of San Francisco Bay also changes seasonally and from year to year.

The U.S. Geological Survey maintains a measurement program to follow changes in some components of water qualtiy, and here we use results of this program to describe some key features of water quality change in the Bay during three recent years. The patterns of water quality variability are displayed as color images that are designed to show the annual cycles of variability, the large year-to-year fluctuation of the annual cycles, and the spatial gradients of water quality in the whole Bay system, from the Sacramento River to the southern South Bay. The three years chosen, 1993-1995, were years of variable weather and precipitation, so they are nice examples for illustrating the effects of changing river flow on water chemistry and biology of the Bay.

Five different descriptors of water quality are shown here, each chosen to indicate the effects of different processes of estuarine variability:

1. The salinity pattern shows the mix between freshwater and seawater, and it is a simple index of the changing effect of river flow on the distribution of dissolved substances.
2. The temperature pattern is a useful indicator of mixing and a habitat descriptor for animals, such as migrating salmon.
3. The patterns of suspended solids show the effect of river flow as a source of new sediments to the Bay.
4. Biological processes at the lowest trophic level are indexed in the patterns of chlorophyll variability, which measures the abundance of phytoplankton (small suspended algae) -- the largest component of living biomass in San Francisco Bay.
5. The patterns of dissolved oxygen reflect the changing balance between photosynthesis (food production) by plants and respiration (food metabolism) by all the organisms living in the Bay.

This water quality program is a collaboration between the U.S. Geological Survey's San Francisco Bay Ecosystem Program and the Regional Monitoring Program for Trace Substances, administered by the San Francisco Estuary Institute.