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Oxygen and carbon isotopic measurements of fossil bivalves (Macoma nasuta) contained in estuarine sediment are used to reconstruct a late Holocene record of salinity and stream flow in San Francisco Bay. Discharge into the bay is a particularly good indicator of paleoclimate in California because the bay's influent streams drain 40% of the state. The isotopic record suggests that between about 1670 and 1900 calendar years (yr cal) B.P. inflow to the bay was substantially greater than the estimated prediversion inflow of 1100 m³/s. An unconformity representing a 900 yr hiatus is present in the core between 1670 and 750 yr cal B.P., possibly caused by a major hydrological event. Over the past 750 yr, stream flow to San Francisco Bay has varied with a period of 200 yr; alternate wet and dry (drought) intervals typically have lasted 40 to 160 yr.