Socio-economic damages caused by extreme floods have been increasing rapidly in recent years, mainly driven by changes in the climate and modulated by increasing human population in deltic areas and floodplains. The Cuvelai-Etosha Basin (CEB) in southern Africa, covering southern Angola and northern Namibia, experiences socially and economically devastating extreme floods. Yet, accurate information on past and current surface water changes and dynamics is lacking. Here, we estimate and map the surface water extents in the CEB and its surroundings (CEB + S) for 32 years (1990–2021) from Landsat data using random forest models to provide long-term baseline information on surface water changes and dynamics. Based on the reference data, a total of 15,677 ± 1080 km2 have been inundated by surface water in the CEB + S during 1990–2021. This extent was accurately mapped by our local water extent product (mapped area = 16,273 km2, user’s accuracy = 91.5 ± 2.5%, producer’s accuracy = 91.1 ± 6%). With user’s and producer’s accuracy of 91%, our overall water extent provides the first most accurate long-term baseline information on surface water inundation in CEB + S necessary for local spatial planning processes to minimise future negative impacts of floods in the basin. Interannual variability of surface water extent is, however, high, with water extent ranging from 520.8 ± 375.7 km2 to 12372.3 ± 1154.7 km2 during the 1990–2021 period. The largest annual water extents (>10,000 km2) were recorded in 2006, 2008, 2009, 2011, and 2017, whereas the smallest extents (<1000 km2) were recorded in 1992 and 2019. We found that over 40% of the area inundated in the CEB + S during 1990–2021 was inundated less than 9 times. With human population increasing rapidly in the CEB + S, rarely inundated areas with short water residence could become a prime target for human settlements, which may lead to huge socio-economic damages during extreme floods if no preventive measures are put in place. Globally available surface water maps from the Global Land Analysis and Discovery (GLAD) and European Commission’s Joint Research Centre (JRC) did not provide realistic surface water extent for CEB + S, especially during years with extreme floods. Therefore, locally adopted product for operational monitoring of surface water in the CEB + S is needed to provide accurate information for informing spatial planning processes and surface water resource management strategies in this endorheic basin and help minimise future negative impacts of floods.