Stampriet Transboundary Aquifer System (STAS) is shared between Botswana, Namibia and South Africa with massive utilization especially in Namibia. However, the understanding of the comprehensive hydrogeological framework of the aquifer system is limited. This study aimed to develop a comprehensive hydrogeological conceptual model of the aquifer system which mainly entailed 3D hydrostratigraphic modelling using Rockworks 3D geological modelling software, analysis of regional groundwater occurrence and flow system, sources and sinks, hydraulic parameters and definition of STAS boundaries. Six hydrostratigraphic units composed of four aquifers, including a new one (the Dwyka), and two aquitards were identified. Analysis of the regional groundwater flow system revealed that groundwater flows in two directions, indicating presence of a regional groundwater divide. 3D hydrostratigraphic geometry revealed that groundwater flow in STAS is influenced by topography but also by faults such as the Zoetfontein Fault, which displaces the pre-Kalahari rocks vertically creating a barrier to groundwater flow. Hydrostratigraphic and 3D geometry work also led to a 42% increase of the size of STAS compared to the boundary initially delineated by UNESCO. The proposed hydrogeological conceptual model forms a basis for development of numerical integrated hydrological model to simulate surface-groundwater interactions, regional groundwater flow and aquifer development potential.