Non-point source pollution risk assessment is an important prerequisite for effective management of watershed water environment. Compared with point source pollution, non-point source pollution often comes from a wide geographical area and a variety of activities, and its impact has strong temporal and spatial variability. Major sources of non-point source pollution include agricultural runoff, urban stormwater runoff, soil erosion, etc. These sources are difficult to monitor and manage individually, so assessing their risks is a critical step in ensuring healthy water quality in a watershed. Understanding the temporal and spatial characteristics of non-point source pollution risk in river basins is essential for developing scientific and effective management strategies. Based on this, this paper studies the risk of non-point source pollution based on water environmental capacity in Wangkuai Reservoir, an important strategic water source in Beijing. Based on the risk assessment method of water environmental capacity (WRA-WEC), the calibrated SWAT model was used to analyze the temporal and spatial distribution characteristics of soil nutrient loss in 6 periods in flood and non-flood seasons in different hydrological years. The main conclusions of paper were listed as follows. 1) The processes of runoff and nutrient (i.e. TN and TP) can be reproduced with good simulation performance for the SWAT model in this watershed. During the calibration period and validation period of the model, Nash-Sutcliffe Efficiency (NSE), Mean Absolute Percentage Error (MAPE), and Coefficient of Determination (R2) of runoff, TN and TP ranged from 0.68-0.93, 0.001-0.007 and 0.76-0.99, respectively. 2) In general, there are differences in the distribution of TN loss risk in different periods. From the perspective of topography, the high risk areas of flood season in wet year are distributed in the eastern part of the basin, and the high risk areas of flood season in normal year and dry year are distributed in the central and southern part of the basin. The high risk areas of non-flood season in wet, normal and dry years are mainly distributed in the northwest and southeast. There were both differences and similarities in the spatial and temporal distribution of TP risk in the six periods. The high risk areas of flood season in flood season of abundant, flat and dry year are distributed in the east, central and south, southwest and northwest respectively, and the high risk areas of other periods are distributed in the northwest and southeast. The pollution risk levels of total nitrogen and total phosphorus and the proportion of high risk areas in different hydrological periods of the same sub-basin are not exactly the same. 3) The effects of pollutant (TN and TP) loss intensity, upstream pollutant input concentration and pollutant water environment capacity on the difference of TN and TP pollution risk value were investigated by redundancy analysis. Redundancy analysis found that the loss risk of TN and TP in this basin is related to pollutant flux, upstream input concentration and water environmental capacity. These driving factors make the pollution risk different in time and space, resulting in the difficulty of pollution control and management. It is necessary to carry out multi-scale Non-point source pollution risk analysis for the upper watershed of Wangkuai Reservoir. The results of this study will provide an effective basis for Non-point source pollution control at the spatial and temporal scale of the basin, and can provide a reference for NPS load reduction and water quality improvement in the basin considering the water environmental capacity.