We investigated physicochemical properties and isotopic compositions of organic matter (δ13CTOC and δ15NTN) in the old fish farming (OFF) site after the cessation of aquaculture farming. Based on this approach, our objective is to determine the organic matter origin and their relative contributions preserved at sediments of fish farming. Temporal and spatial distribution of particulate and sinking organic matter (OFF sites: 2.0 to 3.3 mg L-1 for particulate matter concentration, 18.8 to 246.6 g m-2 day-1 for sinking organic matter rate, control sites: 2.0 to 3.5 mg L-1 for particulate matter concentration, 25.5 to 129.4 g m-2 day-1 for sinking organic matter rate) between both sites showed significant difference along seasonal precipitations. In contrast to variations of δ13CTOC and δ15NTN values at water columns, these isotopic compositions (OFF sites: -21.5‰ to - 20.4‰ for δ13CTOC, 6.0‰ to 7.6‰ for δ15NTN, control sites: - 21.6‰ to - 21.0‰ for δ13CTOC, 6.6‰ to 8.0‰ for δ15NTN) investigated at sediments have distinctive isotopic patterns (p<0.05) for seawater-derived nitrogen sources, indicating the increased input of aquaculture-derived sources (e.g., fish fecal). With respect to past fish farming activities, representative sources (e.g., fish fecal and algae) between both sites showed significant difference (p<0.05), confirming predominant contribution (55.9±4.6%) of fish fecal within OFF sites. Thus, our results may determine specific controlling factor for sustainable use of fish farming sites by estimating the discriminative contributions of organic matter between both sites.