To understand the geochemical characteristics of intertidal sediment in a semi-enclosed bay, we measured various geochemical parameters, including grain size, ignition loss (IL), chemical oxygen demand (COD), acid volatile sulfide (AVS), and trace metals (Al, Fe, Cu, Pb, Zn, Cd, Hg, and As), in intertidal sediment from three bays (Deukryang Bay, Yeoja Bay, and Gamak Bay) in the southern region of Jeollanam Province. The intertidal sediment in Deukryang Bay consisted of various sedimentary types, such as sand, gravelly muddy sand, mud, and silt, whereas the intertidal sediments in Yeoja and Gamak Bays were composed mainly of mud. The concentrations of IL, COD, AVS and trace metals in the intertidal sediments of the three study regions were relatively high near areas affected by input of stream waters and/or shellfish farming waste. The concentrations of organic matter and trace metals in Gamak Bay were much higher than those in Deukryang and Yeoja Bays, which appears to be due to the influence of anthropogenic pollutants, originating from the city and the industrial complex near Gamak Bay. The evaluation results of organic matter and metal pollution using the sediment quality guidelines showed that the intertidal sediments in the three study regions were not polluted in terms of organic matter and trace metals. In future, sustainable management for sources of organic matter and trace metal is necessary to conserve a healthy benthic ecosystem in intertidal sediments.