To optimize the reactive nitrogen cycle in an ecosystem, technologies to increase nitrogen use efficiency and reduce emissions of nitrogen must be developed. In a watershed-ecosystem, land uses with purification abilities can be a powerful tool to mitigate nitrogen loads from non-point sources. This study analyzes the influence of land use on nitrate concentration in the watershed of the Tama River, a typical urban river in Japan. The upstream area is occupied by forest, while the downstream area is dominated by urban land use. In the Tama River watershed, 59% of the total land use is forest; 23% is urban area; and, only 5% is occupied by agricultural land. Urban areas are distributed downstream from the middle reaches. The average nitrate nitrogen (NO3--N) concentration in 2004 increased from upstream to downstream: it was 0.7 mg N L-1 in the upstream area, while it rose to 6.0 mg NO3--N L-1 in the downstream area. The river water NO3--N concentration showed a positive correlation with the proportion of urban land use, while it showed a negative correlation with the proportion of forest. However, some small sub-watersheds have low values for NO3--N concentration despite highly urbanized land use. These sub-watersheds are characterized by higher proportions of paddy rice fields to the total area, ranging from 0.3 to 3.0%, and higher proportions of water body areas, ranging from 8.3 to 30.6%, compared to other sub-watersheds. This might indicate the purification ability of the water bodies and paddy rice fields. Land use within 0 to 50 m from the river water surface influenced water quality and forest and other water bodies reduced nitrate concentration. Construction of artificial wetlands or riparian forests would decrease the N load into the river.