AbstractLarge spatio‐temporal gradients in the Congo basin vegetation and rainfall are observed. However, its water‐balance (evapotranspiration minus precipitation, or ET − P) is typically measured at basin‐scales, limited primarily by river‐discharge data, spatial resolution of terrestrial water storage measurements, and poorly constrained ET. We use observations of the isotopic composition of water vapor to quantify the spatio‐temporal variability of net surface water fluxes across the Congo Basin between 2003 and 2018. These data are calibrated at basin scale using satellite gravity and total Congo river discharge measurements and then used to estimate time‐varying ET − P over four quadrants representing the Congo Basin, providing first estimates of this kind for the region. We find that the multi‐year record, seasonality, and interannual variability of ET − P from both the isotopes and the gravity/river discharge based estimates are consistent. Additionally, we use precipitation and gravity‐based estimates with our water vapor isotope‐based ET − P to calculate time and space averaged ET and net river discharge within the Congo Basin. These quadrant‐scale moisture flux estimates indicate (a) substantial recycling of moisture in the Congo Basin (temporally and spatially averaged ET/P > 70%), consistent with models and visible light‐based ET estimates, and (b) net river outflow is largest in the Western Congo where there are more rivers and higher flow rates. Our results confirm the importance of ET in modulating the Congo water cycle relative to other water sources.