Abstract. Concentrations of recalcitrant and bioavailable dissolved organic carbon (DOC) and their seasonal variations were investigated at three stations in Tokyo Bay, Japan, and in two freshwater sources flowing into the bay. On average, recalcitrant DOC (RDOC), as a remnant of DOC after 150 days of bottle incubation, accounted for 78% of the total DOC in Shibaura sewage treatment plant (STP) effluent, 67% in the upper Arakawa River water, 66% in the lower Arakawa River water, and 78% in surface bay water. Bioavailable DOC (BDOC) concentrations, defined as DOC minus RDOC, were lower than RDOC at all stations. In freshwater environments, RDOC concentrations were almost constant throughout the year. In the bay, RDOC was higher during spring and summer than in autumn and winter because of freshwater input and biological production. The relative concentration of RDOC in the bay derived from phytoplankton, terrestrial, and open-oceanic waters was estimated to be 8–10, 21–32, and 59–69%, respectively, based on multiple regression analysis of RDOC, salinity, and chl a. In addition, comparison with previous data from 1972 revealed that concentrations of RDOC and BDOC have decreased by 33 and 74% at freshwater sites and 39 and 76% in Tokyo Bay, while the ratio of RDOC to DOC has increased. The change in DOC concentration and composition was probably due to increased amounts of STP effluent entering the system. Tokyo Bay exported mostly RDOC to the open ocean because of the remineralization of BDOC.