It is difficult to investigate the factors that control the riverine nitrate-nitrogen (NO3--N) export in a watershed which gains or losses groundwater. To control the NO3--N contamination in these watersheds, it is necessary to investigate the factors that are related to the export of NO3--N that is only produced by the watershed itself. This study was conducted in the Shibetsu watershed located in eastern Hokkaido, Japan, which gains external groundwater contribution (EXT) and 34% of the annual NO3--N loading occurs through EXT. The riverine NO3--N exports from 1980 to 2009 were simulated by the SWAT model, and the factors controlling the temporal and spatial patterns of NO3--N exports were investigated without considering the EXT. The results show that hydrological events control NO3--N export at the seasonal scale, while the hydrological and biogeochemical processes are likely to control NO3--N export at the annual scale. There was an integrated effect among the land use, topography, and soil type related to denitrification process, that regulated the spatial patterns of NO3--N export. The spatial distribution of NO3--N export from hydrologic response units (HRUs) identified the agricultural areas with surplus N that are vulnerable to nitrate contamination. A new standard for the N fertilizer application rate including manure application should be given to control riverine NO3--N export. This study demonstrates that applying the SWAT model is an appropriate method to determine the temporal and spatial patterns of NO3--N export from the watershed which includes EXT and to identify the crucial pollution areas within a watershed in which the management practices can be improved to more effectively control NO3--N export to water bodies.