Integrating hydrology with climate is essential for a better understanding of the impact of present and future climate on hydrological extremes, which may cause frequent flooding, drought, and shortage of water supply. This study assessed the impact of future climate change on the hydrological extremes (peak and low flows) of the Zenne river basin (Belgium). The objectives were to assess how climate change impacts basin-wide extreme flows and to provide a detailed overview of the impacts of four future climate change scenarios compared to the control (baseline) values. The scenarios are high (wet) summer (projects a future with high storm rain in summer), high (wet) winter (predicts a future with high rainfall in winter), mean (considers a future with intermediate climate conditions), and low (dry) (projects a future with low rainfall during winter and summer). These scenarios were projected by using the Climate Change Impact on HYDRological extremes perturbation tool (CCI-HYDR), which was (primarily) developed for Belgium to study climate change. We used the Soil and Water Assessment Tool (SWAT) model to predict the impact of climate change on hydrological extremes by the 2050s (2036–2065) and the 2080s (2066–2095) by perturbing the historical daily data of 1961–1990. We found that the four climate change scenarios show quite different impacts on extreme peak and low flows. The extreme peak flows are expected to increase by as much as 109% under the wet summer scenario, which could increase adverse effects, such as flooding and disturbance of the riverine ecosystem functioning of the river. On the other hand, the low (dry) scenario is projected to cause a significant decrease in both daily extreme peak and low flows, by as much as 169% when compared to the control values, which would cause problems, such as droughts, reduction in agricultural crop productivity, and increase in drinking water and other water use demands. More importantly, larger negative changes in low flows are predicted in the downstream part ...