This study takes Guanshan River Basin, a typical inflow river of the Danjiangkou Reservoir, as the research area, and the nonpoint source (NPS) pollution characteristics of nitrogen and phosphorus from 2013 to 2018 were evaluated by establishing a Soil and Water Assessment Tool (SWAT) model. The pollution characteristics of heavy metals were also evaluated by combining the SWAT and simple output coefficient method. The results show that the pollutant load in Guanshan River Basin contributes significantly to the Danjiangkou Reservoir. Temporally, pollutant loads were primarily concentrated in the flood season, which had a significant positive correlation with precipitation, water yield, and sediments in the abundant period. Among them, sediments were the most important driving factor, followed by water yield. Spatially, pollutant loads were mainly concentrated downstream of the basin, where cultivated land is widespread. In this regard, it is suggested that the input of chemical fertilizers, pesticides, and livestock manure in cultivated land should be controlled and soil erosion downstream of the basin should be prevented to mitigate nitrogen, phosphorus, and heavy metal pollution. This research offers a basis for the formulation and implementation of watershed management for the Danjiangkou Reservoir.