Abstract: Loss of nitrogen and phosphorus from non-point source (NPS) pollution is one of the key drivers of decline in water quality fluctuation of surface water bodies in rural areas. The precise identification of risk zones and site-specific policy for control and management strategies are significant steps for winning the battle against agricultural and rural pollution control. Choosing a typical agricultural production area in Shanghai as the study area, this study obtained the localized export coefficient of NPS pollution discharged at outlets into the river in the plain river network on a monthly scale based on the constructed "hydrological and water quality integrated monitoring system". Combined with geographic information system (GIS) technology and relevant statistical methods, the critical source areas of agricultural NPS pollution were accurately identified. A monthly interval was established for the temporal scale, and irrigation districts were designed as the assessment units for the spatial scale. The equivalent pollutant load discharged per unit area was regarded as the risk zoning assessment index. The study results indicated that cultivation industry was the main source of pollution, contributing 65.43% and 78.69% of the total phosphorus and total nitrogen discharge, respectively. The average equivalent pollutant loads per unit area from May to October were 3.9 (for total nitrogen) and 5.8 times (for total phosphorus) those of other periods, respectively. The cluster analysis results indicated that various assessment units could be categorized into four types from the perspective of the strategies of NPS pollution management: requiring precise fertilization management, requiring balanced land use, requiring differentiated control, and prioritizing aquaculture effluents and orchard fertilization management. In practical engineering, site-specific pollution prevention and control measures can be carefully implemented according to the characteristics of each assessment unit, such as fertilizer ratio optimization, controlled drainage, and the establishment of ecological interception buffer zones, to promote the green and high-quality development of agriculture.