Nitrogen (N) emissions in Asian countries are predicted to increase over the next several decades. An understanding of the mechanisms that control temporal and spatial fluctuation of N export to forest streams is important not only to quantify critical loads of N, N saturation status, and soil acidification N dynamics and budgets in Japanese forested watersheds is not clear due to the lack of regional comparative studies on stream N chemistry. To address the lack of comparative studies, we measured inorganic N (nitrate and ammonium) concentrations from June 2000 to May 2001 in streams in 18 experimental forests located throughout the Japanese archipelago and belonging to the Japanese Union of University Forests. N concentrations in stream water during base flow and high flow periods were monitored, and N mineralization potential in soil was measured using batch incubation experiments. Higher nitrate concentrations in stream water were present in central Japan, an area that receives high rates of atmospheric N deposition. In northern Japan, snowmelt resulted in increased nitrate concentrations in stream water. The potential net N mineralization rate was higher in surface soil than in subsurface soil, and the high potential for N mineralization in the surface soil partly contributed to the increase in nitrate concentration in stream water during a storm event. Regional differences in the atmospheric N deposition and seasonality of precipitation and high discharge are principal controls on the concentrations and variations of nitrates in stream water in forested watersheds of Japan.