The improved representation of inland aquatic (freshwater) and estuarine ecosystems and associated data was a key component of the 2018 National Biodiversity Assessment, and is an essential step in enhancing defensible land use planning and decision making. This paper reports on this enhancement of the National Wetland Map version 5 (NWM5) for South Africa and other data layers associated with the South African Inventory of Inland Aquatic Ecosystems. Detail is provided on (i) the extent of wetlands mapped in NWM5, compared to previous versions of the NWMs; (ii) the improved extent of inland wetlands mapped in focus areas in NWM5 relative to NWM4; (iii) the type of cover associated with the wetlands (inundated, vegetated or arid); (iv) the ecotone between rivers or inland wetlands and estuaries mapped as freshwater-estuarine transition zones; and (v) level of confidence for the inland wetlands in terms of how well the extent and hydrogeomorphic units were captured for each sub-quaternary catchment of South Africa. A total of 4 698 824 ha (3.9% of South Africa) of inland aquatic ecosystems and artificial wetlands have now been mapped, with NWM5 delineating 123% more inland wetlands (2 635 809 ha or 2.2% of SA) compared with NWM4. The estuarine functional zone, which encapsulates all estuarine processes, associated habitats and biota, was refined for 292 systems totalling 188 944 ha, with the addition of 42 micro-estuaries totalling 246 ha. Nearly 600 000 ha (0.5% of SA) of artificial wetlands were mapped in SA. Inland wetlands are predominantly palustrine (55%), some arid (34%) and few inundated systems (11%). Transition zones between freshwater ecosystems and estuaries formed a small fraction (<1.5%) of river total extent (164 018 km), indicating an ecotone where biota and processes continuously vary from freshwater to estuarine. The majority of inland wetlands (~70%) had a low confidence ranking for designation of extent and typing. Future improvements of the map should be focussed on catchment-based improvements particularly in strategic water-source areas, areas of high development pressure and those with low confidence designation of wetland type.