To assess the effects of environmental factors on the sustainability of cultured ark shell Scapharca broughtonii production, we investigated the habitat characteristics of shellfish-farming bays (Gangjin Bay, Yeoja Bay, Keoje Bay and Deukryang Bay). We measured the physiochemical parameters (temperature, salinity, dissolved oxygen, nutrients, chemical oxygen demand and Chlorophyll a) and the geochemical characteristics (chemical oxygen demand, ignition loss, C/N ratio and C/S ratio). Surface sediments were collected from several shellfish-farming bays to examine the geochemical characteristics of both the benthic environment and heavy metal pollution. The grain sizes for Gangjin Bay, Yeoja Bay and Keoje Bay were similar, at the ratio of silt and clay in comparison with Deukryang bay of it. The C/N ratio was more than 5.9, reflecting the range arising from the mix of marine organisms and organic matter. The C/S ratio (more than 4.2) showed that the survey area had anoxic or sub-anoxic bottom conditions. The index of accumulation rate (Igeo) of the metals showed that those research areas can be classified as heavily polluted, heavily to moderately polluted, or more or less unpolluted, respectively. We suggested that the growth of ark shell Scapharca broughtonii in the shellfish-farming bay was effected by the various environmental conditions.