Water is life. It is an important element of the social and economic well-being of society. Kenya is a water-scarce country, ranked as 21st globally for the worst levels of water accessibility. The town of Eldoret is currently experiencing rapid population growth, resulting in ever-growing water demand. On the other hand, climate variability, land cover, and land use changes have altered the hydrologic response of the Kaptagat catchment, one of the major sources of water for Eldoret. This study uses the SWAT model in seeking to evaluate the impact of land use change and climate variability on the catchment yield, resulting in high variations in river flows and storage reservoir levels, and suggests possible mitigation measures to improve the yield. The model was customized for the study area, calibrated, and validated, and simulations were done to establish the changes in yield and river flow over time. This study observes that with time, land use changed due to increased settlement in the catchment, resulting in a decrease in forest cover (natural and planted) from approximately 37% in 1989 to 26% in 2019. Rainfall events also decreased but became more intense. The results of the changing land use and climate variability were changes in the catchment hydrologic response, occasioned by increased surface runoff and decreased baseflow and groundwater recharge, hence the high variations in water levels at the Elegirini and Two Rivers dams in the catchment during the dry and wet seasons, as modeled. The modeling of the catchment management scenarios indicates groundwater recharge increased by 17% and surface runoff decreased by 9%. Therefore, if the ongoing afforestation, reafforestation, and terracing practices by farmers (although small-scale) increasing vegetation cover in the catchment are adhered to, the catchment response regime will improve significantly with time, despite the increasing climatic variability.