Deep learning is a promising method for image classification, including satellite images acquired by various sensors. However, the synergistic use of geospatial data for water body extraction from Sentinel-1 data using deep learning and the applicability of existing deep learning models have not been thoroughly tested for operational flood monitoring. Here, we present a novel water body extraction model based on a deep neural network that exploits Sentinel-1 data and flood-related geospatial datasets. For the model, the U-Net was customised and optimised to utilise Sentinel-1 data and other flood-related geospatial data, including digital elevation model (DEM), Slope, Aspect, Profile Curvature (PC), Topographic Wetness Index (TWI), Terrain Ruggedness Index (TRI), and Buffer for the Southeast Asia region. Testing and validation of the water body extraction model was applied to three Sentinel-1 images for Vietnam, Myanmar, and Bangladesh. By segmenting 384 Sentinel-1 images, model performance and segmentation accuracy for all of the 128 cases that the combination of stacked layers had determined were evaluated following the types of combined input layers. Of the 128 cases, 31 cases showed improvement in Overall Accuracy (OA), and 19 cases showed improvement in both averaged intersection over union (IOU) and F1 score for the three Sentinel-1 images segmented for water body extraction. The averaged OA, IOU, and F1 scores of the ‘Sentinel-1 VV’ band are 95.77, 80.35, and 88.85, respectively, whereas those of ‘band combination VV, Slope, PC, and TRI’ are 96.73, 85.42, and 92.08, showing improvement by exploiting geospatial data. Such improvement was further verified with water body extraction results for the Chindwin river basin, and quantitative analysis of ‘band combination VV, Slope, PC, and TRI’ showed an improvement of the F1 score by 7.68 percent compared to the segmentation output of the ‘Sentinel-1 VV’ band. Through this research, it was demonstrated that the accuracy of deep learning-based water body extraction from Sentinel-1 images can be improved up to 7.68 percent by employing geospatial data. To the best of our knowledge, this is the first work of research that demonstrates the synergistic use of geospatial data in deep learning-based water body extraction over wide areas. It is anticipated that the results of this research could be a valuable reference when deep neural networks are applied for satellite image segmentation for operational flood monitoring and when geospatial layers are employed to improve the accuracy of deep learning-based image segmentation.