Diatoms from cores collected in northern San Francisco Bay marshes have been used to reconstruct a late Holocene record of river flow in the Sacramento-San Joaquin River drainage. The coring sites are located between the normal marine environment of San Francisco Bay and the freshwater environment of the Sacramento and San Joaquin Rivers. Variation in the discharge from these rivers is an indication of both the volume and timing of precipitation over more than 40% of California.

The composition of modern diatom assemblages in freshwater, brackish, and saltwater marshes is used to calibrate the late Holocene salinity record. Variation in taxonomic composition of the entire diatom assemblage, as well as a simplified biometric which summarizes the relationship between salinity and individual taxa, are used as proxies for river flow. Dominant taxa in each assemblage vary down core, indicating that variation in salinity is only one parameter in a complex set of physical and chemical factors that control the temporal and spatial distribution of diatoms in northern San Francisco Bay marshes.

At the Rush Ranch coring site there appears to be evidence of salinity cycles over the past 3,000 years. Prior to European contact about 150 years ago, there are two intervals dominated by freshwater taxa and two intervals dominated by more marine taxa. The intervals that indicate more saline conditions (3,000 cal yr B.P. to 2,500 cal yr B.P. and 1750 cal yr B.P. to 750 cal yr B.P.) may correspond to periods of lower precipitation suggested by other California climate records. Smaller-scale variations within the salinity cycles correlate with variations in the lake level record at Mono Lake, as well as shorter precipitation cycles in the Sierra Nevada. Carbon isotope and pollen records from the Rush Ranch marsh corroborate the diatom evidence.