Coastal sediments accumulate organic matter (OM) from diverse sources, including local anthropogenic pollution. Effective source tracking of sediment OM is crucial for pollution source management. This study compares fluorescence proxies and stable isotopic ratios as tracers for sediment OM in Gangu Port, Korea. An optimized extraction method using distilled water for 0.5 h yielded distinct fluorescence signatures. The humification index (HIX) and protein-like component (C3%) showed ideal mixing behavior with two end-members (fishery market sediment and algae). A Bayesian end-member mixing analysis model revealed that agricultural soil is the prevalent contributor to sediments, aligning with land use patterns. The fluorescence-based model showed higher sensitivity to anthropogenic influences compared to traditional stable isotope ratios. The results strongly agreed with isotope ratio-based predictions, exhibiting a positive correlation (p < 0.05) at 8 out of 14 sites. This study highlights the potential of fluorescence-based tracking to complement or replace conventional stable isotope methods.