Our knowledge of the spatio-temporal variation of river hydrological parameters is surprisingly poor. In situ gauge stations are limited in spatial and temporal coverage, and their number has been decreasing during the past decades. On the other hand, remote sensing techniques have proven their ability to measure different parameters within the Earth system. Satellite imagery, for instance, can provide variations in river area with appropriate temporal sampling. In this study, we develop an automatic algorithm for water body area monitoring based on maximum a posteriori estimation of Markov random fields. The algorithm considers pixel intensity, spatial correlation between neighboring pixels, and temporal behavior of the water body to extract accurate water masks. We solve this optimization problem using the graph cuts technique. We also measure the uncertainty associated with the determined water masks. Our method is applied over three different river reaches of Niger and Congo rivers with different hydrological characteristics. We validate the obtained river area time series by comparing with in situ river discharge and satellite altimetric water level time series. Along the Niger River, we obtain correlation coefficients of 0.85–0.96 for river reaches and 0.65 for the Congo River, which is demonstrably an improvement over other river mask retrieval algorithms.