River water quality was evaluated with respect to eutrophication and land use during spring snowmelt and summer base flow periods in Abashiri (mixed cropland-livestock farming) and Okoppe (grassland-based dairy cattle farming), eastern Hokkaido, Japan. Water from rivers and tributaries was sampled during snowmelt and summer base flow periods in 2005, and river flow was measured. Total N (TN), NO(3)-N, and Si concentrations were determined using standard methods. Total catchment and upland areas for each sampling site were determined with ArcGIS hydrology modeling software and 1:25,000-scale digital topographic maps. Specific discharge was significantly higher during snowmelt than during base flow. In both areas, TN concentrations increased, whereas Si concentrations decreased, with increased specific discharge, and were significantly higher during snowmelt. The Si:TN mole ratio decreased to below or close to the threshold value for eutrophication (2.7) in one-third of sites during snowmelt. River NO(3)-N concentrations during base flow were significantly and positively correlated with the proportion of upland fields in the catchment in both the Abashiri (r = 0.88, P < 0.001) and Okoppe (r = 0.43, P < 0.01) areas. However, the regression slope, defined as the impact factor (IF) of water quality, was much higher in Abashiri (0.025) than in Okoppe (0.0094). The correlations were also significantly positive during snowmelt in both areas, but IF was four to eight times higher during snowmelt than during base flow. Higher discharge of N from upland fields and grasslands during snowmelt and the resulting eutrophication in estuaries suggest that nutrient discharge during snowmelt should be taken into account when assessing and monitoring the annual loss of nutrients from agricultural fields.