The floods are an annual phenomenon on the Pacific Coast of Ecuador and can become devastating during El Niño years, especially in the Guayas watershed (32,300 km²), the largest drainage basin of the South American western side of the Andes. As limited information on flood extent in this basin is available, this study presents a monitoring of the spatio-temporal dynamics of floods in the Guayas Basin, between 2005 and 2008, using a change detection method applied to ENVISAT ASAR Global Monitoring SAR images acquired at a spatial resolution of 1 km. The method is composed of three steps. First, a supervised classification was performed to identify pixels of open water present in the Guayas Basin. Then, the separability of their radar signature from signatures of other classes was determined during the four dry seasons from 2005 to 2008. In the end, standardized anomalies of backscattering coefficient were computed during the four wet seasons of the study period to detect changes between dry and wet seasons. Different thresholds were tested to identify the flooded areas in the watershed using external information from the Dartmouth Flood Observatory. A value of −2.30 ± 0.05 was found suitable to estimate the number of inundated pixels and limit the number of false detection (below 10%). Using this threshold, monthly maps of inundation were estimated during the wet season (December to May) from 2004 to 2008. The most frequently inundated areas were found to be located along the Babahoyo River, a tributary in the east of the basin. Large interannual variability in the flood extent is observed at the flood peak (from 50 to 580 km²), consistent with the rainfall in the Guayas watershed during the study period.