Generating aerial shoreline segmentation masks can be a daunting task, often requiring manual labeling or correction. This is further problematic because neural segmentation models require decent and abundant data for training, requiring even more manpower to automate the process. In this paper, we propose utilizing Unmanned Surface Vehicles (USVs) in an automated shoreline segmentation system on satellite imagery. The remotely controlled vessel first collects above- and underwater shoreline information using light detection and ranging (LiDAR) and multibeam echosounder (MBES) measuring instruments, resulting in a geo-referenced 3D point cloud. After cleaning and processing these data, the system integrates the projected map with an aerial image of the region. Based on the height values of the mapped points, the image is segmented. Finally, post-processing methods and the k-NN algorithm are introduced, resulting in a complete binary shoreline segmentation mask. The obtained data were used for training U-Net-type segmentation models with pre-trained backbones. The InceptionV3-based model achieved an accuracy of 96% and a dice coefficient score of 93%, demonstrating the effectiveness of the proposed system as a source of data acquisition for training deep neural networks.