We analyzed bioavailability, photoreactivity, fluorescence, and isotopic composition of dissolved organic carbon (DOC) collected at 13 stations in the Sacramento–San Joaquin River Delta during various seasons to estimate the persistence of DOC from diverse shallow water habitat sources. Prospective large-scale wetland restorations in the Delta may change the amount of DOC available to the food web as well as change the quality of Delta water exported for municipal use. Our study indicates that DOC contributed by Delta sources is relatively refractory and likely mostly the dissolved remnants of vascular plant material from degrading soils and tidal marshes rather than phytoplankton production. Therefore, the prospective conversion of agricultural land into submerged, phytoplankton-dominated habitats may reduce the undesired export of DOC from the Delta to municipal users. A median of 10% of Delta DOC was rapidly utilizable by bacterioplankton. A moderate dose of simulated solar radiation (286Wm−2 for 4h) decreased the DOC bioavailability by an average of 40%, with a larger relative decrease in samples with higher initial DOC bioavailability. Potentially, a DOC-based microbial food web could support ≤0.6נ109g C of protist production in the Delta annually, compared to ≈17נ109g C phytoplankton primary production. Thus, DOC utilization via the microbial food web is unlikely to play an important role in the nutrition of Delta zooplankton and fish, and the possible decrease in DOC concentration due to wetland restoration is unlikely to have a direct effect on Delta fish productivity.