This work aims to validate the wide use of an algorithm developed using genetic programing (GP) techniques allowing to discern between water and non-water pixels using the near infrared band and different thresholds. A total of 34 wetlands and shallow lakes of 18 ecological types were used for validation. These include marshes, salt ponds, and saline and freshwater, temporary and permanent shallow lakes. Furthermore, based on the spectral matching between Landsat and Sentinel-2 sensors, this methodology was applied to Sentinel-2 imagery, improving the spatial and temporal resolution. When compared to other techniques, GP showed better accuracy (over 85% in most cases) and acceptable kappa values in the estimation of water pixels (κ ≥ 0.7) in 10 of the 18 assayed ecological types evaluated with Landsat-7 and Sentinel-2 imagery. The improvements were especially achieved for temporary lakes and wetlands, where existing algorithms were scarcely reliable. This shows that GP algorithms applied to remote sensing satellite imagery can be a valuable tool to monitor water coverage in wetlands and shallow lakes where multiple factors cause a low resolution by commonly used water indices. This allows the reconstruction of hydrological series showing their hydrological behaviors during the last three decades, being useful to predict how their hydrological pattern may behave under future global change scenarios.