We investigated geochemical properties, and microbial sulfate- and iron(III) reduction in sediment influenced by the aquaculture of abalone in the Nohwa-do, southern coastal sea in Korea. Concentrations of ammonium, phosphate, and sulfide in the pore-water were higher at farm sites than at control sites. The differences between the 2 types of sites were most apparent in terms of the weights of abalone and the temperature increase during September. Accordingly, the rates of sulfate reduction at the farm sites during September (61 mmol S $m^{-2}d{-1}$) were 3-fold higher than the sulfate reduction during May (20 mmol S $m^{-2}d{-1}$). In contrast, Fe(III) reduction rates were highest at the control sites in May, but its significance was relatively decreased at farm sites during September when sulfate reduction rates were highest. During September, benthic ammonium flux was 3-fold greater at the farm sites (35 mmol N $m^{-2}d{-1}$) than at the control sites (12 mmol N $m^{-2}d{-1}$), and phosphate flux was 8-fold higher at the farm sites (0.018 mmol P $m^{-2}d{-1}$) than at control sites (0.003 mmol P $m^{-2}d{-1}$). Overall results indicated that the inappropriate operation of a large-scale aquaculture farm may result in excess input of biodeposits and high nutrient fluxes from the sediment, thereby decreasing diversity of the benthic ecosystem and deepening eutrophication in coastal waters.