Floods are the most common and expensive natural calamity, affecting every country. Flooding in the Shebelle River Basin (SRB) in southern Somalia has posed a significant challenge to sustainable development. The main goal of this study was to analyze flood hazard, vulnerability and risk in the part of SRB using GIS-based Multi-Criteria Decision Analysis (MCDA). The flood hazard map was constructed using seven important causative factors: elevation, slope, drainage density, distance to river, rainfall, soil and geology. The results demonstrate that very low, low, moderate, high, and very high flood hazard zones correspond to 10.92%, 24.97%, 29.13%, 21.93% and 13.04% of the area of SRB, respectively. The flood vulnerability map was created using five spatial layers: land use/land cover, population density, distance to road, Global man-made impervious surface (GMIS), and Human built-up area settlement extent (HBASE). In addition, the results of the flood susceptibility and vulnerability maps were used to create a flood risk map. The results demonstrate that for the Shebelle River Basin, 27.6%, 30.9%, 23.6%, 12.1%, and 5.7% area correspond to very low, low, moderate, high, and very high flood risk zones, respectively. The Receiver Operating Characteristics-Area Under the Curve (ROC-AUC) of the flood hazard model exhibited a good prediction accuracy of 0.781. The majority of the basin is at risk of flooding in the very low, low, and moderate ranges; however, some tiny areas are at risk of flooding in the high and very high ranges. Flood hazard, vulnerability and risk maps should be provided and distributed the authorities responsible for flood protection so that people are aware flood risk locations.