Hydrological alterations can reduce aquatic biodiversity by disrupting the life cycles of organisms. However, past studies have faced difficulties in quantifying the impacts of dams and climate change, which are major drivers of hydrological alterations. Here, we aimed to evaluate and compare the hydrological alterations caused by dams and climate change throughout the Omaru River catchment, Japan, using a distributed hydrological model (DHM). First, to assess the impacts of dam and climate change independently, we performed runoff analyses using either dam discharge or future climatic data (two future periods, 2031-2050 and 2081-2100 × three representative concentration pathways). Subsequently, we derived indicators of hydrologic alterations (IHA) to quantify changes in flow alterations by comparing them to IHA under natural conditions (i.e., without dam or climate change data). The runoff analysis was calibrated and validated by comparing with daily streamflow at a site with minimal effects of substantial abstraction, and showed high reproducibility from 2010 to 2019 (Nash-Sutcliffe efficiency = 0.921–0.964). We found that dams altered IHAs more than climate change. However, on a catchment-scale standpoint, climate change induced wider ranges of flow alterations, such as low flow metrics along the tributaries and uppermost main stem, suggesting a catchment-level shrinkage in important corridors of aquatic organisms by reducing upstream length and water level. We also observed that the altered flow by water withdrawals were ameliorated by the confluence of tributaries and downstream hydropower outflows. Our approach using a DHM captured the various patterns of flow alterations by dams and climate change.