Stakeholder-informed approach improves national modelling of water resources for a sub-Saharan African basin

•Study area: Lake Malawi Shire River Basin (LMSRB), Southern Africa •Study focus: 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). •New hydrological insights for the region: Model modifications, including simulation of sanitation usage (specifically pit latrines) and wetland simulation, significantly improved streamflow simulation performance; the unmodified model had 71 % adequate streamflow simulation, increasing to 89 % following stakeholder-informed modifications. Modelling national water resources in other southern African countries should consider similar modifications. Our model shows a consistent decline in groundwater levels since 1980 (the beginning of our study period). We estimate an annual decrease of 0.59 km³ (approximately 0.1 %) in groundwater storage in Malawi from 1980 to 2009, raising significant concerns about the country’s future water security. This model provides unprecedented insight into Malawi’s water security, particularly regarding the unseen but critical groundwater resource.