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In the Congo Basin, the elevated vulnerability of food security and the water supply implies that sustainable development strategies must incorporate the effects of climate change on hydrological regimes. However, the lack of observational hydro-climatic data over the past decades strongly limits the number of studies investigating the effects of climate change in the Congo Basin. We present the largest altimetry-based dataset of water levels ever constituted over the entire Congo Basin. This dataset of water levels illuminates the hydrological regimes of various tributaries of the Congo River. A total of 140 water level time series are extracted using ENVISAT altimetry over the period of 2003 to 2009. To improve the understanding of the physical phenomena dominating the region, we perform a K-means cluster analysis of the altimeter-derived river level height variations to identify groups of hydrologically similar catchments. This analysis reveals nine distinct hydrological regions. The proposed regionalization scheme is validated and therefore considered reliable for estimating monthly water level variations in the Congo Basin. This result confirms the potential of satellite altimetry in monitoring spatio-temporal water level variations as a promising and unprecedented means for improved representation of the hydrologic characteristics in large ungauged river basins.