This study assessed the impact of intensive human activities on organic matter (OM) and heavy metal cycles in Shihwa Lake, South Korea. Sediment oxygen demand (SOD), benthic nutrient flux (BNF), and benthic heavy metal flux were estimated using in situ benthic chambers. The combined analysis of sediment trap and SOD showed that the vertical supply of OM was a major controlling factor for benthic respiration. The BNF accounted for 35–144% and 32–184% of the N and P required, respectively, for primary production (PP) in the water column. The higher SOD may have also accelerated the release of Mn, Fe, Co, and Ni from the sediment. Benthic fluxes of Cr, As, Cd, Pb, Cu, and Zn were highest near the industrial complex, with ranges of 1.3 ± 0.9, 6.4 ± 4.9, 0.2 ± 0.1, 0.5 ± 0.4, 7.7 ± 1.4, and 452 ± 133 μmol m⁻² d⁻¹, respectively. Mn, Fe, Co, As, Pb, Ni, and Cu contributed more than 10% of the sediment to the current standing stock at Shihwa Lake.