Hydrological processes in tropical watersheds are increasingly influenced by land use/land cover (LULC) change and climate variability, with particularly severe consequences where such basins supply water to urban centres. This study assessed the individual and combined impacts of LULC and climate variability on the hydrology of the Mulunguzi River Basin (MRB), a critical water source in southern Malawi, over the period 1990–2020. The Soil and Water Assessment Tool (SWAT) was applied and showed satisfactory model performance (NSE = 0.59, R2 = 0.62, RSR = 0.64). Trends in climate variables were evaluated using the Mann–Kendall test at α=0.05 significance level. The results show increasing temperature (0.004 °C month−1; 0.041 °C year−1) and rainfall (5.8 mm year−1), although these trends were not statistically significant at α=0.05 level. During the study period, forest cover declined by 24.04%, resulting in a 119.9% increase in surface runoff and a 17.8% reduction in baseflow, indicating diminished groundwater recharge. Climate variability alone increased surface runoff by 152%, while the combined effects of LULC and variability produced even stronger hydrological responses than either factor acting independently. These results demonstrate that deforestation and a warming, wetter climate are jointly amplifying runoff while weakening dry-season flows, thereby increasing flood risk and reducing water security. The findings underscore the urgent need for integrated land management and climate adaptation strategies to ensure the long-term sustainability of water resources in the MRB.