Floods are one of the most frequent natural disasters worldwide. Although the vulnerability varies from region to region, all countries are susceptible to flooding. Mozambique was hit by several cyclones in the last few decades, and in 2019, after cyclones Idai and Kenneth, the country became the first one in southern Africa to be hit by two cyclones in the same raining season. Aiming to provide the local authorities with tools to yield better responses before and after any disaster event, and to mitigate the impact and support in decision making for sustainable development, it is fundamental to continue investigating reliable methods for disaster management. In this paper, we propose a fully automated method for flood mapping in near real-time utilizing multi-temporal Sentinel-1 Synthetic Aperture Radar (SAR) data acquired in the Beira municipality and Macomia district. The procedure exploits the processing capability of the Google Earth Engine (GEE) platform. We map flooded areas by finding the differences of images acquired before and after the flooding and then use Otsu’s thresholding method to automatically extract the flooded area from the difference image. To validate and compute the accuracy of the proposed technique, we compare our results with the Copernicus Emergency Management Service (Copernicus EMS) data available in the study areas. Furthermore, we investigated the use of a Sentinel-2 multi-spectral instrument (MSI) to produce a land cover (LC) map of the study area and estimate the percentage of flooded areas in each LC class. The results show that the combination of Sentinel-1 SAR and Sentinel-2 MSI data is reliable for near real-time flood mapping and damage assessment. We automatically mapped flooded areas with an overall accuracy of about 87–88% and kappa of 0.73–0.75 by directly comparing our prediction and Copernicus EMS maps. The LC classification is validated by randomly collecting over 600 points for each LC, and the overall accuracy is 90–95% with a kappa of 0.80–0.94.