The Shirakami Mountain range, including the largest primeval beech forest in East-Asia, is undergoing ecological change. Dissolved organic matter (DOM) plays an important role in nutrient and material cycling in forest ecosystems. Because the quality of DOM varies based on its origin and diagenetic and runoff processes, changes in the environment surrounding DOM can be rapidly detected by monitoring its quality. Herein, concentrations and fluorescence composition of DOM at 14 sites in 13 streams in the Shirakami Mountain range were monitored monthly for over 2 years, excluding winter (December–March), to gain insight into the catchment hydrological and soil characteristics affecting DOM concentrations and composition in stream water. Based on the pattern of temporal changes in fluorescent component composition, monitoring sites were categorized into four groups (streams with small catchments, large catchments, catchments facing the Sea of Japan, and open waters in the catchment) with similar catchment characteristics affecting DOM dynamics. Multiple linear regression analysis showed that DOM concentrations in each group could be attributed to rainfall on the survey date, short-term (1–2 days) rainfall, midterm (~1 month) accumulated rainfall, midterm (7–11 days) accumulated temperature, and catchment characteristics as explanatory variables. The degree of influence of these variables differed among the four groups. The results of this study show that grouping streams according to catchment hydrological characteristics can help identify the impact of climate and environmental change on DOM dynamics in stream water.