Stable carbon isotopes and fossil pollen found in local marsh sediments are used to reconstruct the paleosalinity for the northern reaches of the San Francisco Bay Estuary. We combine these two methods to overcome the ambiguities inherent in each. Changes detected in the plant assemblages of local brackish marshes are used as indicators of changes in paleosalinity. Two high salinity events have been detected in the combined records from Brown’s Island (near the mouth of the Sacramento San Joaquin Delta) occurring at c. 868 cal. B.P. and 1226 cal. B.P. Previous studies from Brown’s Island were not able to detect these salinity events and the site was not considered sensitive enough to salinity changes. Combined isotope and pollen records from other local marshes in the North Bay fill in the salinity history for this part of the Estuary.