Thirty-eight aquifer units are shared between Malawi and its neighbouring countries. It is essential to prioritize those transboundary aquifers that require immediate attention. A methodology of identifying hotspots in the transboundary aquifers of Malawi that may be at risk of depletion or contamination has been developed. There are 11 local-scale and three national-scale hotspots of transboundary concern in Malawi. Fiscal and planning measures can now be taken to assess these areas in more detail, fostering transboundary cooperation between stakeholders at both local and national scales.