During floods, updated and accurate information on affected human settlements helps save lives and reduces time to rescue. Therefore, approaches that can provide reliable information during floods via the use of all-weather and real-time functional technology is highly needful. The study presented here attempts to efficiently and precisely map villages in the Indian sub-continent during floods via a three-stage approach which uses PolSAR data. However, an accurate segregation of villages in India even with PolSAR data is challenging because the built-up structures in the villages of rural India are closely placed and are randomly oriented w.r.t. each other. This condition either hinders their segregation or otherwise induces false alarms during extraction. More descriptive land cover characterization features and powerful feature classifiers may address this challenge. The study in this paper proposes a novel approach to efficiently detect and map flood affected villages which utilize polarization signatures from PolSAR imagery, ensemble-of -dilated-convolutions based CNNs, apriori knowledge and image morphology. The approach broadly involves three stages: first, built-up area extraction from a PolSAR image: second, detection of villages in a built-up area image and third, identification and mapping of villages that are affected by the flood. In the first stage, an ensemble of varying dilated-convolutions based novel CNN classifier which directly utilizes PolSAR-2 polarization signatures (PSs) in window-mode as features are developed to extract built-up areas. The second stage provides a novel village detection filter based on apriori knowledge and image morphology to detect actual villages and mask out the false objects. Finally, in the third stage, flood affected villages are mapped via a series of morphological operations based degree-of-intersection measure. Experiments are conducted on both simulated and natural flooded area datasets. Experimental results show 81% detection accuracy and 100% mapping performance of the proposed approach which indicates its potential as an effective flood affected village mapping system.