Abstract: The eutrophication situation in the nearshore waters of Liaodong Bay is severe, especially the problem of excessive water pollution near the important estuary at the bottom of the bay. Therefore, it is of great significance to explore the spatiotemporal distribution characteristics of river pollution entering the sea and its impact on the water quality of nearshore waters for the management of river basins and seawater environments. This study takes Xiaoling river as an example and applies the LOADEST model to estimate the fluxes of several typical pollutants from Xiaoling river into the sea in 2022. Moreover, a Bohai water quality model developed based on the HAMSOM model was applied to conduct in-depth analysis of the relationship between typical pollutant flux changes of Xiaoling river and the response of sea water quality. The results indicate that the monthly flux of pollutants from Xiaoling river into the sea shows an upward trend followed by a downward trend. Due to the influence of runoff and agricultural breeding period, the total phosphorus, potassium permanganate index, and ammonia nitrogen monthly inflow in July were the highest, at 30.38 t, 910 t, and 222 t, respectively. The analysis of water quality response in Bohai Sea shows that the flux of pollutants entering the sea in the basin significantly affects the water quality of nearshore waters. The highest pollution concentration and the largest impact range in the estuary area from July to August are consistent with the peak pollution flux of Xiaoling river. However, the evolution patterns of water quality response zones for different pollutants vary. Based on the calculation results of the pollution sharing rate of Xiaoling river, it is found that in order to improve the water quality of the nearshore waters in the long run, various pollutants should be given equal attention. Moreover, when formulating corresponding pollution control measures, differential management should be fully considered for different pollution source sharing rates.