In the production of a digital orthophoto map (DOM) from unmanned aerial vehicle (UAV)-acquired overlapping images, some anomalies such as texture stretching or data holes frequently occur in water areas due to the lack of significant textural features. These anomalies seriously affect the visual quality and data integrity of the resulting DOMs. In this study, we attempted to eliminate the water surface anomalies in an example DOM via replacing the entire water area with an intact one that was clipped out from one single UAV image. The water surface scope and boundary in the image was first precisely achieved using the multisource seed filling algorithm and contour-finding algorithm. Next, the tie points were selected from the boundaries of the normal and anomalous water surfaces, and employed to realize their spatial alignment using affine plane coordinate transformation. Finally, the normal water surface was overlaid onto the DOM to replace the corresponding anomalous water surface. The restored water area had good visual effect in terms of spectral consistency, and the texture transition with the surrounding environment was also sufficiently natural. According to the standard deviations and mean values of RGB pixels, the quality of the restored DOM was greatly improved in comparison with the original one. These demonstrated that the proposed method had a sound performance in restoring abnormal water surfaces in a DOM, especially for scenarios where the water surface area is relatively small and can be contained in a single UAV image.