Semi-enclosed coastal bays are highly susceptible to eutrophication because restricted water exchange promotes the accumulation and recycling of nutrients and organic matter. Jinhae Bay (JB), a representative embayment on Korea's southern coast, supports extensive mariculture in its western inner bay, while its northeastern margins are influenced by urban and industrial catchments. Despite comprehensive measures to reduce nutrient inputs from wastewater and aquaculture, long-term ecosystem responses to these regulations remain poorly understood. Using a 15-year (2011–2025) monitoring dataset from the Korea Marine Environment Management Corporation, we examined decadal variability in nutrient dynamics across JB subregions. The most coherent trends were organic matter enrichment and nitrogen loss at the bay-wide scale, which together drove a significant increasing trend in the ratio of chemical oxygen demand (COD) to total nitrogen (TN) in all subregions. The two bay types differed, however, in how this trend emerged: the mariculture-dominated bays showed the largest COD increases without a concurrent decline in TN, whereas the urbanized bays combined rising COD with significant declines in TN and total organic nitrogen. Together, these patterns implied that contemporary nutrient dynamics in JB are regulated not only by external loading but also by internal regeneration and changes in the bulk composition of organic matter pools. These findings advance understanding of the long-term biogeochemical evolution of eutrophic, semi-enclosed coastal ecosystems and provide a scientific basis for adaptive management under continuing anthropogenic and climate-driven pressures.