Improving our understanding of groundwater resources is essential for effective management and sustainable development. Here, we apply a global hydrological model, the Community Water Model (CWatM, 5 arc minute resolution) with MODFLOW6 (5 km resolution), to gain understanding of Malawi’s understudied groundwater resources. The study applies semi-structured stakeholder interviews to inform simulation of water management in a data scarce context. Model simulation was validated against streamflow data for 35 rivers. Basin-wide scale model validation was undertaken by comparison with remote sensing observations of evapotranspiration, precipitation, and changes in total water storage (using GRACE Satellite data).