River inflow and suspended-sediment flux to San Francisco Bay are dominated by the Sacramento and San Joaquin River systems. Suspended sediments collected from rivers within the Sacramento and San Joaquin drainage basins show distinct chemical and Sr isotope signatures, reflecting their distinct bedrock lithologies. Concentrations of Sm, Nd, K, and Rb and 87Sr/86Sr ratios in suspended sediments increase from north to south in Sierra Nevada rivers and are significantly higher in the San Joaquin drainage than in the Sacramento drainage. We show that variations in the geochemistry of fine-grained detrital sediments cored beneath the bay can be used to assess the relative contributions of suspended sediment and inflow from these two major drainages in California. For the sampled intervals over the past 1850 yr, the proportion of suspended sediment from the Sacramento drainage relative to the San Joaquin drainage ranged between 5% and 85% (average value of 55%), compared with a modern value of ∼91%. The current predominance of sediment entering San Francisco Bay from the Sacramento drainage may be the result of greater trapping of sediments by reservoirs within the San Joaquin drainage basin. Changes in the relative proportion of sediment from the Sacramento and San Joaquin drainages may reflect changes in the position of the storm track over California.