Hydrological alterations, which can be represented by the extent of the changes in the flow patterns resulting from anthropogenic factors, 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. 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 × three representative concentration pathways; RCPs). 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 analyses showed high reproducibility throughout the study period (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 watershed-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, which used a distributed hydrological model, developed a better understanding of flow alterations by dams and climate change.