Studying the pressing impacts of climate change on runoff is vital for the sustainable functioning of society and ecosystems. In Senegal, there is insufficient consideration given to the magnitude of the decrease in water resources caused by climate change and the potential impact of this decrease on both society and the environment. The objective of this study was to evaluate the hydrological effects of climate change in the Aga-Foua-Djilas basin by employing CWatM hydrological models inside the frameworks of ISIMIP and HMF-WA. Over the historical period (1981–2019) in the Aga-Foua-Djilas basin, the analysis of all hydrological parameters indicates positive trends, although not statistically significant (except for runoff). Over the future period, unlike temperatures and PET, which show an upward trend in all scenarios, precipitation and runoff show downward trends, which are more significant under SSP 585. For precipitation, Kendall’s Tau shows a downward trend of − 0.157 mm/yr, − 0.321 mm/yr, and − 0.472 mm/yr under SSP 126, SSP 370 and SSP 585, respectively. For runoff, the trends are negative and of the order of − 0.207 m3/s/yr, − 0.44 m3/s/yr, and − 0.565 m3/s/yr, respectively, under SSP 126, SSP 370 and SSP 585 with CwatM and − 0.248 m3/s/yr (SSP 126), − 0.389 m3/s/yr (SSP 245) and − 0.579 m3/s/yr (SSP585) with HMF-WA. Compared with the decrease in precipitation toward the end of the century, the decrease in runoff noted for the distant future (2081–2100) will be of the order of − 32.8% (SSP 126), − 80.8% (SSP 370) and − 94.6% (SSP 585) with CwatM and − 22.3% (SSP 126), − 19.6% (SSP 245) and − 50.9% (SSP 585) with HMF-WA. This study could help policymakers and stakeholders to develop adaptation strategies for the Aga-Foua-Djilas basin.