The Congo River Basin (CRB) is the second largest river system in the world, but its hydroclimatic characteristics remain relatively poorly known. Here, we jointly analyze a large record of in situ and satellite-derived observations, including long term time series of Surface Water Height (SWH) from radar altimetry (a total of 2,311 virtual stations) and surface water extent (SWE) from a multi-satellite technique to better characterize CRB surface hydrology and its variability. Firstly, we show that SWH from radar altimetry multi-missions agree well with in situ water stage at various locations, with root mean square deviation varying from 10 cm (with Sentinel-3A) to 75 cm (with European Remote Sensing-2). SWE from multi-satellite observations also shows a good behavior over a ~25-year period against in situ observations from sub-basin to basin scale. Both datasets help to better characterize the large spatial and temporal variability of hydrological patterns across the basin, with SWH exhibiting annual amplitude of more than 5 m in the northern sub-basins while Congo main-stream and Cuvette Centrale tributaries vary in smaller proportions (1.5 m to 4.5 m). Furthermore, SWH and SWE help better illustrate the spatial distribution and different timings of the CRB annual flood dynamic and how each sub-basin and tributary contribute to the hydrological regime at the outlet of the basin (the Brazzaville/Kinshasa station), including its peculiar bi-modal pattern. Across the basin, we jointly use SWH and SWE to estimate time lag and water travel time to reach the Brazzaville/Kinshasa station, ranging from 0–1 month in its vicinity downstream the basin up to 3 months in remote areas and small tributaries. Northern sub-basins and the central Congo region highly contribute to the large peak in December–January while the southern part of the basin supplies water to both hydrological peaks, in particular to the moderate one in April–May. The results are supported using in situ observations at various locations in the basin. Our results contribute to a better characterization of the hydrological variability in the CRB and represent an unprecedented source of information for hydrological modeling and to study hydrological processes over the region.