To identify the factors controlling the distribution of dissolved organic carbon (DOC) in the northern Ariake Sea (Japan), we measured DOC, salinity and chlorophyll a (Chl. a) along transect lines from the largest river discharging into the Ariake Sea (the Chikugo River) to the opposite shore. The DOC concentration was significantly correlated with salinity, although no correlation was found between the Chl. a concentration and DOC. Thus, river inflow is the primary source of DOC. However, the expected concentration of riverine DOC, represented by the y-intercept of the regression curve between salinity and DOC, was much higher than the DOC concentration of the Chikugo River, suggesting the presence of additional DOC sources to the Ariake Sea. We conducted particulate organic matter (POM) decomposition experiments and observed DOC production after incubation. Thus, microbial POM decomposition may be a source of excess DOC. This study is the first to show that river inflow and microbial decomposition of POM affect the DOC distribution in the northern Ariake Sea.