Concerns have been raised regarding the degradation of stream water quality due to the excessive influx of atmospheric deposition. This study aimed to reveal the long‐term variation in stream water chemistry in approximately 40 forested small watersheds in the northern Kanto region, based on 3 surveys conducted in 1991–1992, 2006–2007, and 2022. The factors influencing each dissolved element were investigated. Regarding long‐term variations in stream water chemistry, relatively stable concentrations of cations (Ca2+, Mg2+, K+, and Na+) and SiO2 were observed. However, the concentrations of anions (Cl−, , and ) decreased due to the improvement in the atmospheric environment and the diminishing effect of fertilization. Furthermore, the recent increase in stream water pH was attributed to an increase in bicarbonate (), compensating for the decrease in anion concentrations relative to cations. Geology was the most significant factor for inter‐watershed variations in cations and SiO2, and this influence remained relatively constant over 30 years. Forest practices, especially fertilization, had a significant effect on Cl− and , and contributed to higher concentrations in the fertilized watersheds than in the non‐fertilized watersheds over the 15 years following fertilization. Sulfate deposition was a significant influencing factor for , and the concentration fluctuated under long‐term variations in deposition over the past 30 years. Despite substantial acid deposition in the study area, the absence of stream water acidification could be attributed to the abundant cation supply from bedrock and volcanic ash, which underwent weathering processes.