•A national border based approach to transboundary aquifer assessments is proposed.•Transboundary aquifers must be conceptualized as hydraulically connected systems.•Conceptual models are an effective way to portray these complex systems.•Transboundary aquifer systems must be managed locally and regionally in Malawi. Malawi. Integrated water resource management (IWRM) of transboundary aquifers (TBA’s) is becoming increasingly important. Without adequate and accurate scientific knowledge of their extent and characteristics, uninformed policy creation could lead to unsustainable management of these vital resources. This is particularly important within the Southern African Development Community (SADC) where up to 85% of domestic water is supplied by groundwater. In this paper, Malawi is used as a case study to critically evaluate the current transboundary aquifer assessment frameworks within the region and their value in promoting IWRM. A series of illustrative conceptual models of TBA interactions pertinent to the Malawian national border are presented and we consider how TBA assessments may be integrated to national IWRM and strategic policy development. Current TBA assessments of Malawi and the wider SADC neglect multiple aspects needed for a national scale management plan. This includes full border TBA system identification alongside, given the geology of the region, consideration of the discontinuous nature of basement complex aquifers and localised alluvial deposits that both result in smaller scale aquifer units. Conceptualising such local scale complexity and encouraging countries to develop a strategy that systematically examines TBA systems along their national border at relevant scales will allow for more focused conjunctive policy creation and sustainable management of TBA’s.