Angola is a source of many major rivers in southern Africa and is referred to as the “water tower” of the region. The lack of a defined area delineating the Angolan Highlands water tower (AHWT) limits the conservation of this important freshwater source. This study hydrologically defines the boundary of the AHWT as areas > 1274 m above mean sea level within the Central Bié Plateau of Angola. Using the Climate Hazards Group InfraRed Precipitation with Station (CHIRPS) data, this study provides a 41-year precipitation budget of the AHWT and surrounding basins. Between 1981 and 2021, the average annual precipitation over the AHWT was 1112 mm and the gross annual average precipitation volume was approximately 423 km3over an area of 380,382 km2. The AHWT is the southern source of the Congo Basin, the western source of the Zambezi Basin, and the sole water source of the endorheic Okavango Basin and Okavango Delta, a UNESCO World Heritage Site. On average, approximately 133 km3(92.36%) of the gross annual precipitation volume for the headwater Cuito and Cubango catchments of the Okavango River is lost before reaching the Okavango Delta. Estimates of the annual flooding of the Okavango Delta during a 35-year period (1985–2019) were correlated to precipitation in the headwater catchments. Correlation coefficients are stronger for the entire rainfall season (0.76) and early rainfall season (0.62) for the combined Cuito–Cubango catchment in comparison to late rainfall season (0.50), which suggests that the antecedent conditions (first and second flood pulse) during the early rainfall season allows for greater Okavango Delta flood inundation. The correlation coefficients between the Cubango (0.72) and Cuito (0.78) Rivers and annual flood inundation are not significantly different (P> 0.05); however, these rivers have fundamental hydrological differences that influence the functioning of the Okavango Delta. The Cubango River, described as a flushing system, has much steeper gradient, more compact and shallow soils and flows faster with significant rapids, whereas the peatland rich, absorbent, seepage-driven baseflow of the Cuito River sustains the Okavango Delta during the dry season. The dynamics of seasonal precipitation, hydrology and climate change in the AHWT have important repercussions on water budgets, food security and biodiversity throughout southern Africa, requiring continued collaboration between countries to ensure that future development is sustainable.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10661-023-11448-7.