To understand the status of organic matter and heavy metal pollution in surface sediment of a fish farming area, we have measured the concentrations of total organic carbon (TOC), total nitrogen (TN), and heavy metals (As, Cd, Cr, Cu, Fe, Hg, Mn, Pb, and Zn) in surface sediments of a fish farming area near Tongyoung-Geoje coast. The mean concentrations of TOC and TN were 22.7 mg/g and 3.4 mg/g, respectively, and were much higher than those in surface sediments of a semi-enclosed bay in the southern coast of Korea. The mean concentrations of As, Cd, Cr, Cu, Fe, Hg, Mn, Pb, and Zn were 10.5 mg/kg, 0.37 mg/kg, 82.9 mg/kg, 127 mg/kg, 4.19%, 0.041 mg/kg, 596 mg/kg, 39.5 mg/kg, and 175 mg/kg, respectively, and the mean concentrations of Cd and Cu were three times higher than those in surface sediments of shellfish farming area in the southeastern coast of Korea. In addition, the concentrations of TOC and corrected Cu exceeded the values of sediment quality guidelines applied in Korea, and pollution load index (PLI) and ecological risk index (ERI) showed that the metal concentrations in the sediments of some fish farming area have a strongly negative ecological impact on benthic organisms, although most metal concentrations did not exceed the sediment quality guidelines. Based on overall assessment results, the surface sediments of fish farming areas in the study region are polluted with organic matter and some heavy metals. Thus, a comprehensive management plan is necessary to improve the sedimentary environments, identify primary contamination sources, and reduce the input of pollution load for organic matter and heavy metals in the sediments of fish farming areas.