Fertilizer input for agricultural food production, as well as the discharge of domestic and industrial water pollutants, increases pressures on locally scarce and vulnerable water resources in the North China Plain. In order to: (a) understand pollutant exchange between surface water and groundwater, (b) quantify nutrient loadings, and (c) identify major nutrient removal pathways by using qualitative and quantitative methods, including the geochemical model PHREEQC) a one-year study at a wheat (Triticum aestivum L.) and maize (Zea mays L.) double cropping system in the Baiyang Lake area in Hebei Province, China, was undertaken. The study showed a high influence of low-quality surface water on the shallow aquifer. Major inflowing pollutants into the aquifer were ammonium and nitrate via inflow from the adjacent Fu River (up to 29.8mg/L NH4-N and 6.8mg/L NO3-N), as well as nitrate via vertical transport from the field surface (up to 134.8mg/L NO3-N in soil water). Results from a conceptual model show an excess nitrogen input of about 320kg/ha/a. Nevertheless, both nitrogen species were only detected at low concentrations in shallow groundwater, averaging at 3.6mg/L NH4-N and 1.8mg/L NO3-N. Measurement results supported by PHREEQC-modeling indicated cation exchange, denitrification, and anaerobic ammonium oxidation coupled with partial denitrification as major nitrogen removal pathways. Despite the current removal capacity, the excessive nitrogen fertilization may pose a future threat to groundwater quality. Surface water quality improvements are therefore recommended in conjunction with simultaneous monitoring of nitrate in the aquifer, and reduced agricultural N-inputs should be considered.