Sources and sinks of organic carbon for San Francisco Bay (California, USA) were estimated for 1980. Sources for the southern reach were dominated by phytoplankton and benthic microalgal production. River loading of organic matter was an additional important factor in the northern reach. Tidal marsh export and point sources played a secondary role. Autochthonous production in San Francisco Bay appears to be less than the mean for temperate-zone estuaries, primarily because turbidity limits microalgal production and the development of seagrass beds. Exchange between the Bay and Pacific Ocean plays an unknown but potentially important role in the organic carbon balance. Interannual variability in the organic carbon supply was assessed for Suisun Bay, a northern reach subembayment that provides habitat for important fish species (delta smelt Hypomesus transpacificus and larval striped bass Morone saxatilus). The total supply fluctuated by an order of magnitude; depending on the year, either autochthonous sources (phytoplankton production) or allochthonous sources (riverine loading) could be dominant. The primary cause of the year-to-year change was variability of freshwater inflows from the Sacramento and San Joaquin rivers, and its magnitude was much larger than long-term changes arising from marsh destruction and point source decreases. Although interannual variability of the total organic carbon supply could not be assessed for the southern reach, year-to-year changes in phytoplankton production were much smaller than in Suisun Bay, reflecting a relative lack of river influence.