Assessing the impacts of climate change and land use/land cover changes on water resources within a catchment is essential because it helps us understand how these dynamic factors affect the quantity, quality, and availability of freshwater. This knowledge is crucial for making informed decisions about water management, conservation, and adaptation strategies, especially in regions facing increasing environmental uncertainties and challenges to water resource sustainability. In Pakistan’s Kunhar River Basin (KRB), this investigation explores the potential effects of shifting land use/land cover (LULC), and climate on stream flows. The SWAT (Soil and Water Assessment Tool), a semi-distributed hydrological model, and the most recent Coupled Model Intercomparison Project phase 6 (CMIP6) dataset from multiple global climate models (GCMs) were used to evaluate these effects. The temperature and precipitation data were downscaled using the CMhyd software; for both shared socioeconomic pathways (SSP2 and SSP5), the top-performing GCM out of four was required to produce downscaled precipitation and temperature predictions while taking future land use characteristics into account. The output from the chosen GCM indicated that by the conclusion of the 21st century, relative to the reference period (1985–2014), the study area’s average monthly precipitation, highest temperature, and lowest temperature will be increasing. Precipitation is anticipated to increase between 2015 and 2100 by 20.5% and 29.1% according to the SSP2 and SSP5 scenarios, respectively. This study’s findings, which emphasize the need for project planners and managers taking into account the effects of climate and land cover changes in their management techniques, show that climate change can have a significant impact on the changing seasons of flows in the Kunhar River basin.