Water body extraction is significant for flood disaster monitoring using satellite imagery. Conventional methods have focused on finding an index, which highlights water body and suppresses nonwater body such as vegetation or soil area. The Normalized Difference Water Index (NDWI) is typically used to extract water body from satellite images. The drawback of NDWI, however, is that some man-made objects in built-up areas have NDWI values similar to water body. The objective of this paper is to propose a new method that could extract correctly water body with built-up areas in before and after images of flood. We first create a two-element feature vector consisting of NDWI and a Near InfRared band (NIR) and then select a training site on water body area. After computing the mean vector and the covariance matrix of the training site, we classify each pixel into water body based on Mahalanobis distance. We also register before and after images of flood using outlier removal and triangulation-based local transformation. We finally create a change map by combining the before-flooding water body and after-flooding water body. The experimental results show that the overall accuracy and Kappa coefficient of the proposed method were 97.25% and 94.14%, respectively, while those of the NDWI method were 89.5% and 69.6%, respectively.