Organic enrichment was investigated in surface sediments from the Yeoja and Gangjin Bays of Korea, which contain dense shellfish farms, in order to evaluate the contamination status and temporal changes in shellfish farming along these coasts. The degree of organic enrichment was determined using geochemical indicators (chemical oxygen demand, ignition loss, acid volatile sulfide, total organic carbon in sediments, and total nitrogen in sediments, ammonium and nitrate in pore water, and bioluminescence inhabitation for sediments). Temporal changes in organic enrichment conditions were detected by comparing our 2012 data to those previously reported from a survey conducted in 1999/2000. Organic enrichment was significantly higher in September than in May and July, in Gangjin Bay than in Yeoja Bay, and significantly higher in shellfish farms than in reference sites not used to culture shellfish. Ammonium concentrations in pore water were two orders of magnitude greater than nitrate concentrations, suggesting that these bays represent nitrogen-reducing environments.