Groundwater serves as a critical resource for sustaining livelihoods and ecosystems, yet many regions—including the Lake Victoria Basin (LVB)—lack sufficient borehole observations to characterize aquifer dynamics. This chapter addresses this data gap by developing a knowledge-based framework that integrates the GLDAS Catchment Land Surface Model (CLSM) with supplementary rainfall, hydrological, topographical, and geological datasets to assess groundwater variability and storage potential. Our methodology employs factor analysis and inversion techniques to demonstrate that GLDAS CLSM outputs reliably capture: (1) seasonal recharge patterns (peaking in March-May and September-November), (2) spatial storage differences (greater potential in western highlands versus southeastern lowlands), and (3) geological controls (limited storage in areas with resistant basement rocks). Validation against water balance equations confirms the model’s ability to reproduce expected hydrogeological behaviors, offering a practical solution for groundwater assessment in data-scarce tropical basins.