Burundi is susceptible to future water-related disasters, but examining the influence of climate change on regional hydroclimatic features is challenging due to a lack of local data and adaptation planning. This study investigated the influence of climate change on hydroclimate-focused changes in the climatology of heavy precipitation (and streamflow) means and extremes based on the multi-model ensemble mean of earth system models in the sixth phase of the Coupled Model Intercomparison Project (CMIP). For runoff analysis, hydrologic responses to future climate conditions were simulated using the Soil and Water Assessment Tool (SWAT) model over the Ruvubu River basin, Burundi. Temperature increases by 5.6 °C, with strong robustness, under future climate conditions. The mean annual precipitation (and runoff) undergoes large seasonal variations, with weak robustness. Precipitation (and streamflow) changes between the wet and dry seasons differ in signal and magnitude. However, alterations in both the amount and frequency of precipitation reveal the intensification of the water cycle due to anthropogenic climate change. Thus, the highest variability in the maximum daily streamflow is shown in months of long wet seasons, especially in the far future (2085). Without considering the regional climate characteristics and shared socioeconomic pathway (SSP) scenarios, this behavior is expected to be enhanced in 2085 (compared with 2045) and increase the severity of extreme precipitation and flood risk. Climate change will cause alterations in the magnitude and seasonal distributions of extreme precipitation (and streamflow). These findings could be important for flood planning and mitigation measures to cope with climate change in Burundi.