Weekly water quality measurements and 15 intensive surveys during rainy days were conducted for 8 years in two coniferous forest watersheds (a watershed with delayed thinning and a reference). There is a tendency that the pollutant load runoffs from the watershed with delayed thinning were higher than those of the reference. In addition, thinning practice leaving abandoned lumber increased the base flow rate due to the absence of evapotranspiration by trees, and consequently the base flow load increased. These results suggest that the effect of delayed thinning in coniferous plantations is important for river water quality and eutrophication of lakes. This is because delayed thinning leads to a closed canopy that prevents sunlight from reaching the forest floor and undergrowth disappears, and the nutrient-rich soil surface would be subject to erosion.