The stable carbon and nitrogen isotopic compositions (δ13C and δ15N) of sedimentary organic matter (OM) in fish farms (FFs) were investigated to quantify the aquaculture-derived OM deposition dynamics in the sediment. The dual isotopic compositions of mixed OMs in surface sediments at FFs differed significantly (p < 0.05) from those at reference sites, indicating an increased deposition of fish feces or uneaten feed in the sediments. Furthermore, OM source apportionments revealed that the quantitative contribution of fish feces (23.3 mg g−1 dw) during farming activities was significantly higher than that of other natural OM sources (C3 plants and phytoplankton). After the disassembly of fish cages, the deposited fish feces may be preferentially degraded through processes that require a large amount of oxygen consumption (<0.1 kg C m−2 yr−1). Our isotopic approach may be helpful for assessing the impact of FF wastes and for taking measures to minimize environmental deterioration.