Understanding the spatial distribution and sources of sedimentary organic matter (OM) in coastal environments is crucial for effective water quality management and the preservation of ecosystem health. Although extensive research has been conducted on OM dynamics, there remains a gap in understanding the ongoing biogeochemical processes in Korean coastal aquaculture zones, particularly during the summer season. To address this gap, we investigated the spatial variation of water chemical properties and isotopic composition of sedimentary OM to trace the composition, source, and reactivity of mixed OM in aquaculture systems along the Korean coast during the summer season. The isotopic approach was applied to surface sediments from five sections: western (W)-1, W-2, southern (S)-1, S-2, and eastern (E)-1. With respect to increased nutrients (mainly nitrate; 1.2 ± 0.6 mg/L) by dam-water discharge near W sections, our isotopic signatures revealed that a substantial fraction of sedimentary OM might dominantly originated from autochthonous OM source (algae; 36.5%) related to the increase of terrestrial nutrients. Simultaneously, the deposition of allochthonous OM (aquacultural feces; 44%) was predominant in the S-2 sections. The 34S-depleted patterns (approximately -7.2‰) in the S-2 section was indicative of active sulfate reduction occurring at the sedimentary boundary. Therefore, together with the precise determination of ongoing OM, our isotopic results provide valuable insights for effectively managing water-sedimentary qualities under the increase of anthropogenic contamination.