Groundwater pollution risk assessment in the groundwater source field (GSF) is crucial to ensure groundwater quality safety. A systematic method of assessing groundwater pollution in the GSF was established by combining the numerical models of groundwater flow and solute transport in the vadose zone and aquifer. It is featured by revealing the paramount fate of contaminant from the surface to receptor "well (wells)" via the pathway of vadose zone and aquifers. The method was verified in the phreatic and semi-confined aquifers of a vital GSF, Beijing-Tianjin-Hebei region (BTHR) in China. Nitrate was selected as the model pollutant. The results indicated that the groundwater pollution risk of the phreatic aquifer was dominated by the mediate level (45.27%), and that the second semi-confined aquifer was mainly ranked as relatively low (30.29%) and mediate (38.17%) levels. The groundwater pollution risk maps of the two aquifers were similar. The high and relatively high risk areas were affected by the high intensities of groundwater pollution sources (GPSIs) or short distances from the pollution sources to the pumping well. The low and relatively low risk areas were controlled by low GPSIs and adequate attenuation and denitrification of nitrate in the aquifer. The groundwater pollution risk in the semi-confined aquifer was lower than that in the phreatic aquifer. The groundwater pollution risk mapping provides a valuable scientific reference for the groundwater pollution prevention and control with the focus on the "pollution source" and "groundwater source field". The proposed method can be further applied to the protections of the GSFs in the BTHR.