Abstract: This study evaluates the spatial distribution of nitrogen(N) and phosphorus(P) pollution in a segment of the Xi'er River, from its control gate to the first dam, which is the natural outflow of the Erhai Lake in Yunnan Province. Through field sampling and analysis of overlying water and surface sediments, the study provides a reference for dredging and substrate restoration in the river channel. The results show that in the study area, the concentrations of total nitrogen(TN) and total phosphorus(TP) in the overlying water ranged from 0.56 to 0.91 mg/L(mean: 0.71 mg/L) and 0.027 to 0.033 mg/L(mean: 0.030 mg/L), respectively. In the surface sediments, the concentrations of TN and TP ranged from 1 250 to 3 090 mg/kg(mean: 2 390 mg/kg) and 443 to 906 mg/kg(mean: 698 mg/kg), respectively. The findings indicate that while the surface sediments are severely polluted with N and P, there is no significant correlation between the pollution levels in the overlying water and the sediments. Localized spatial variations of N and P in the sediments are associated with the growth of submerged macrophytes, such as Vallisneria natans, Hydrilla verticillata, and Ceratophyllum demersum. To ensure the positive development of the aquatic ecosystem in the Xi'er River, it is recommended to shift the management strategy for pollutant load reduction from traditional river dredging to ecological restoration by increasing the coverage of submerged macrophytes to purify the surface sediments.