The water chemistry of a stream reflects the biogeochemical processes occurring in upstream forests. Anthropogenic disturbances in forests, such as cutting of trees, altering the nitrogen (N) cycle, and increase in N leaching from the soil to streams, potentially cause acidification or eutrophication downstream. In forests with dense understory vegetation, mechanical site preparation following tree cutting is commonly used to improve the early establishment of tree seedlings. In cool-temperate forests in northern Hokkaido, Japan, dense understory vegetation (mainly comprising Sasa dwarf bamboo) inhibits forest regeneration after tree cutting. Soil scarification is a common site preparation technique for eliminating Sasa bamboo and improving forest regeneration. Long-term data are useful for examining the temporal changes in stream water chemistry exposed to different specific forest management practices under changing environment (e.g., climate change and atmospheric N deposition). For 14 years (2003–2016), we observed the stream water chemistry in naturally forested watersheds and at one point after the confluence of all streams in Uryu Experimental Forest of Hokkaido University (North Hokkaido Experimental Forests Site of JaLTER) in northern Japan. We also monitored stream discharge, water level, and stream water temperature in each watershed. Water samples were collected from the outlets of ten watersheds. The forest management practice in each watershed includes clear-cutting, soil scarification in sparse forest with dense understory Sasa, and clear-cutting and soil scarification followed by soil replacement. Long-term data in the six unmanaged watersheds are also valuable as a background information to analyze the effect of long-term climate, environment, and vegetation changes on stream water chemistry. The measured water quality data of 1,873 water samples include the ion concentrations (Cl-, NO3-, SO42-, Na+, NH4+, K+, Mg2+, and Ca2+), pH, and electrical conductivity (EC) in the stream water. The range of the concentrations of Cl-, NO3-, SO42-, Mg2+, and Ca2+ in the stream water across all the watersheds throughout the observed periods (minimum to maximum) were 3.35 to 23.67, 0.01 to 8.68, 0.83 to 4.01, 0.45 to 2.55, and 0.72 to 6.16 mg L-1, respectively. Similarly, the stream pH and EC ranged from 6.04 to 7.53 and 3.14 to 9.47 mS m-1, respectively.