<p>Land cover, along with climate change and variability, plays a vital role in influencing hydrological patterns and regimes. This study examines the impact of land cover and climate variability on stream flow in the Kikuletwa catchment, Pangani Basin, Tanzania; using historical data, Sentinel-2 images, CMIP6 climate mode and the Soil and Water Assessment Tool (SWAT). Results indicates significant land cover changes with cropland increasing from 25.6 to 31.7%, shrubland decreasing from 0.3 to 0.10%, and dense vegetation increasing from 11.9 to 15.2%. Urbanization increases by 28.5% and vegetation decreases by 7.4%. The SWAT was calibrated and validated with coefficient of determination values of 0.63 and 0.60, Nash-Sutcliffe efficiency values of 0.62 and 0.58, and PBIAS values of − 40 and − 15% respectively; the negative PBIAS indicates model underestimation. Future scenarios (RCP 4.5 and 8.5) are projected for 2039 and 2059; warming trends and seasonal fluctuations in precipitation are detected with a significant urban growth and shifts in vegetation patterns. Predicted changes in streamflow show increased flows (300–1500 m³/s) during wet months and decreased flows (100–375 m³/s) during dry periods. Stream flow under future climate scenarios indicate that both climate and land cover changes significantly impact streamflow. Also, for the streamflow analysis under RCP 4.5 and RCP 8.5 for 2020–2039 p-values and t-values ranges from 0.066 to 0.070 and − 2.042 to − 2.006 respectively while for 2040–2059 p-values and t-values ranges from 0.424 to 0.769 and 0.301 to 0.830 respectively. The results offer insights for sustainable water resource management, with an underscore of the need for proactive water resource planning and management to address expected changes. Recommendations emphasize integrated water management, improved modelling, land cover change monitoring, community engagement, and resilience strategies.</p>