Flooding in urban areas is counted as a significant disaster that must be correctly mitigated due to the huge amount of affected people, material losses, hampered economic activity, and flood-related diseases. One of the technologies available for disaster mitigation and prevention is satellites providing image data on previously flooded areas. In most cases, floods occur in conjunction with heavy rain. Thus, from a satellite’s optical sensor, the flood area is mostly covered with clouds which indicates ineffective observation. One solution to this problem is to use Synthetic Aperture Radar (SAR) sensors by observing backscatter differences before and after flood events. This research proposes mapping the flood-prone areas using machine learning to classify the areas using the 3D CNN method. The method was applied on a combination of co-polarized and cross-polarized SAR multi-temporal image datasets covering Jakarta City and the coastal area of Bekasi Regency. Testing with multiple combinations of training/testing data proportion split and a different number of epochs gave the optimum performance at an 80/20 split with 150 epochs achieving an overall accuracy of 0.71 after training in 283 min.