To improve the accuracy and automation of extracting water body by using remote sensing image, a method was proposed for water body extraction based on Stacked AutoEncoder (SAE). A deep network model was built by stacking sparse autoencoders and each layer was trained in turn with the greedy layerwise approach. Features were learnt without supervision from the pixel level to avoid the problem that methods such as traditional neural network needed artificial feature analysis and selection. Softmax classifier was trained with supervision by using the learnt features and corresponding labels. Back Propagation (BP) algorithm was used to fine-tune and optimize the whole model. The accuracy of SAE-based method reaches 94.73% by using the Tarim River's ETM+ data to do the experiment, which is 3.28% and 4.04% higher than that of Support Vector Machine (SVM) and BP neural network separately. The experimental results show that the proposed method can effectively improve the accuracy of water body extraction.