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The potential response of flow regimes to future climate has crucial importance for a variety of practical applications, such as sustainable water management and ecological asset preservation. For this study, multi-site investigations of alterations in flow regimes under projected climate change were performed for one of the largest watersheds in Morocco, the Bouregreg Watershed (BW). Future daily streamflow was simulated using the eco-hydrological model Soil and Water Assessment Tool (SWAT) forced by climatic data from CMIP5 model outputs. Simulations were carried out for two periods: 2035–2050 (2040s), and 2085–2100 (2090s) under two emissions scenarios: RCP4.5 and RCP8.5. Future streamflow regimes were examined in accordance with an Indicators of Hydrologic Alteration (IHA) analysis, while being confronted with baseline flow data. Mean temperature has been predicted to increase by up to 2.79 °C in the 2090s (RCP8.5), and a higher variability in rainfall regime is expected. The results indicate that, under future changes in climate patterns, flow regimes in BW will be altered. However, the extent of alteration will be reflected unevenly among the four streams of the study watershed. The IHA analysis revealed that most of the river network will experience both a decrease in monthly flow magnitude (mostly in November and December), and an increase (dominantly in February and March) when compared to baseline. The frequency of flash pulses, and the number of zero-flow days are also expected to increase. Most of the projected alterations were estimated to become very significant in the 2090s under the RCP8.5 scenario. The potential ecological implications were also analysed, and the most sensitive streams of BW were identified to guide local water planning and ecological preservation strategies. • SWAT, CMIP5 data and IHA method used to forecast future flow regimes in Morocco. • Alterations extent will be unevenly distributed over the river network. • Ecological implications are expected due to climate change impact on flow attributes. [ABSTRACT FROM AUTHOR]