Human activities have intensified the global challenge of coastal eutrophication. Recently, water resource managers have encountered difficulties in formulating precise pollutant reduction strategies to mitigate coastal eutrophication. Despite the recognized importance of coastal wetlands and pollution sources in influencing coastal nutrient levels, accurately quantifying their impact remains difficult. To address this challenge, this study introduces a novel approach for optimizing water environmental capacity. A coupled model integrating hydrodynamics, water quality, and wetland nutrient mechanisms was developed to simulate the spatio-seasonal distribution of water, sediment, and vegetation nutrients in a semi-enclosed bay (Liaodong Bay, China) and a large-scale coastal wetland (Liaohe estuary wetland, China). Model parameters and simulation results were calibrated and validated using extensive long-term field investigations and laboratory experiments. The average root mean square errors between simulated and observed values for all validation points were as follows: 0.80mgL-1, 0.53mgL-1, 0.08mgL-1, 6.70μgL-1, and 0.50μgL-1 for dissolved oxygen, chemical oxygen demand, dissolved inorganic nitrogen, dissolved inorganic phosphorus, and chlorophyll-a, respectively. The total nitrogen (TN) and total phosphorus (TP) in the sediment were 0.10gkg-1 and 0.05gkg-1, respectively. For Suaeda salsa, the TN and TP were 2.91gkg -1 and 0.08gkg -1, respectively. For Phragmites australis, the TN and TP were 114.22gkg -1 and 6.21gkg -1, respectively. The results suggest that excessive river discharge and a stable residual circulation structure contribute to the persistent eutrophication in Liaodong Bay. The Liaohe estuary wetland enhances the environmental capacity of dissolved inorganic nitrogen and dissolved inorganic phosphorus in Liaodong Bay to 271±31tyr-1 and 8±1tyr-1, respectively, accounting for 1.8±0.2% and 1.3±0.2% of their respective environmental capacities. The reduction in dissolved inorganic nitrogen concentration is significant, with a maximum decrease of 0.17mgL-1. The maximum contributions of atmospheric deposition and aquaculture wastewater to dissolved inorganic nitrogen concentration are 0.08mgL-1 and 0.03mgL-1, respectively, with higher contributions in spring and summer than in fall and winter. These findings highlight the critical role of coastal wetlands in mitigating eutrophication and underscore the need for spatio-seasonal water management programs. This work serves as a model for effectively reducing global coastal pollution emissions.