We measured dissolved and particulate organic carbon (DOC and POC) in samples collected along 13 transects of the salinity gradient of Chesapeake Bay. Riverine DOC and POC end-members averaged 232±19 μM and 151±53 μM, respectively, and coastal DOC and POC end-members averaged 172±19 μM and 43±6 μM, respectively. Within the chlorophyll maximum, POC accumulated to concentrations 50–150 μM above those expected from conservative mixing and it was significantly correlated with chlorophylla, indicating phytoplankton origin. POC accumulated primarily in bottom waters in spring, and primarily in surface waters in summer. Net DOC accumulation (60–120 μM) was observed within and downstream of the chlorophyll maximum, primarily during spring and summer in both surface and bottom waters, and it also appeared to be derived from phytoplankton. In the turbidity maximum, there were also net decreases in chlorophylla (−3 μg l−1 to −22 μg l−1) and POC concentrations (−2 μM to −89 μM) and transient DOC increases (9–88 μM), primarily in summer. These occurred as freshwater plankton blooms mixed with turbid, low salinity seawater, and we attribute the observed POC and DOC changes to lysis and sedimentation of freshwater plankton. DOC accumulation in both regions of Chesapeake Bay was estimated to be greater than atmospheric or terrestrial organic carbon inputs and was equivalent to ≈10% of estuarine primary production.