Coastal evolution is influenced by past sea-level changes and resultant shifts from fluvial- to marine-dominant environments and the accompanying significant geochemical and isotopic changes in the water mass and sediments. We investigated the elemental and isotopic features of coastal sedimentary cores (27 m in length) from a small paleo-bay located on the southern coast of Korea to determine such geochemical variability and specify past changes in the bay environment and anoxic conditions and possible links to past climate changes. We analyzed total organic carbon (TOC), total sulfur (TS), their isotopes (δ13CTOC and δ34STS), and pyrite. The δ13CTOC values ranging from −25 to −19‰ (a proxy for terrestrial influence) were lower than average (−22.5‰) before 8300 cal yr BP and since 500 cal yr BP, while the intervening Early to Late Holocene showed higher δ13CTOC values, indicating a shallow coastal environment. The δ34STS values fluctuating between −35 and +5‰ resembled sedimentation rate change. Based on the changes in the ratios of TOC to TS (C/S ratios), sedimentation rate, and δ34STS, we found five possible periods with higher salinity and intensified anoxic conditions at millennial timescales: 8900–8200, 7950–6500, 5200–4300, 3500–2600, and 2000–1100 cal yr BP. These intensified anoxic conditions seem to have been influenced by increased air temperature and sea-surface temperature conditions, which could have intensified the intensity of thermal stratification (less ventilation and mixing) between surface and bottom waters and resultant anoxic conditions.