To assess the nitrogen pollution load potential (NPLP) of groundwater, mass balance over a recent five-year period (2006–2010) was analyzed within the Tedori River alluvial fan area, Ishikawa Prefecture, Japan. All components of the hydrologic cycle in polluted regions of the study area were analyzed based on water and nitrogen balance. The water balance model was based on the exchange of river water between the channel/soil surface and the aquifer horizon fractions. The water balance calculation was conducted by considering precipitation, evapotranspiration, direct runoff, and infiltration in the channel/soil horizon (Figure 2). In addition, infiltration from paddy and other land uses, recharge and effluent from the Tedori River and pumping from the wells in the aquifer horizon were considered. Based on the water balance analysis, nitrogen balance analysis was conducted. The results revealed that the nitrogen input was 1,214.2 ton/year, while nitrogen output was 959.4 ton/year. Therefore, 254.6 ton/year accumulated within the study area. In the aquifer horizon, the amount of nitrogen deposited was found to be 232.9 ton/year. The total nitrogen concentration of water samples collected from a well with a depth of 50 m was about 1.0 mg/L, which was greater than that observed for the well of 150 m depth (about 0.25 mg/L). These findings indicate that contaminating nitrogen gradually percolates into the deeper zone. The most dominant nitrogen pollutant for the study area originated from farmland (30.5%) and second is intake water (24.2%) and third is precipitation (23.8%). These three items occupied 78.5% of total pollutant.