The use of unmanned aerial systems (UASs) has increased tremendously in the current decade. They have significantly advanced remote sensing with the capability to deploy and image the terrain as per required spatial, spectral, temporal, and radiometric resolutions for various remote sensing applications. One of the major advantages of UAS imagery is that images can be acquired in cloudy conditions by flying the UAS under the clouds. The limitation to the technology is that the imagery is often sullied by cloud shadows. Images taken over water are additionally affected by sun glint. These are two pose serious issues for estimating water quality parameters from the UAS images. This study proposes a novel machine learning approach first to identify and extract regions with cloud shadows and sun glint and separate such regions from non-obstructed clear sky regions and sun-glint unaffected regions. The data was extracted from the images at pixel level to train an U-Net based deep learning model and best settings for model training was identified based on the various evaluation metrics from test cases. Using this evaluation, a high-quality image correction model was determined, which was used to recover the cloud shadow and sun glint areas in the images.