A Windows-based system for estimating the potential nitrogen (N) outflow in a catchment has been developed. The system includes a conversion method for administrative-based data from national scale statistics, such as the agricultural census, into a catchment-based data by utilizing the geographic information system (GIS). The system calculates N loads based on the pollutant load unit (PLU) method in a catchment and converts them to potential N outflows by introducing the outflow coefficients. For the catchments of tributaries flowing into Lake Kasumigaura in central Japan, where nonpoint sources were predominant, the N loads and the potential N outflows from 1950 to 1995 were estimated. The actual N outflows from the tributaries were also estimated using the water quality monitoring data at the outlet of the tributary catchment and meteorological data. These potential N outflows and actual N outflows were compared. Results obtained were as follows. (i) Some estimates by the present method, such as the drainage area and cultivation areas of various crops in each tributary, well agreed with those estimated by other methods and published data, indicating that this method was capable of estimating catchment-based data from the administrative-based statistics. (ii) Changes in the potential outflows during the period from 1950 to 1995 reflected the changes in livestock production and methods of waste water treatments. (iii) Comparison between the N potential outflows and the actual N outflows suggested that about 47% of the generated N load which leached down to groundwater from the soil surface flowed out and that a time-lag between two outflows appeared. Thus, the developed system offered good possibilities of realistic quantitative analyses on the contribution of non-point sources to water quality on the scale of a catchment.