This study presents an innovative approach to automated coral reef monitoring using satellite imagery, addressing challenges in image quality assessment and correction. The method employs Principal Component Analysis (PCA) coupled with clustering for efficient image selection and quality evaluation, followed by a machine learning-based cloud removal technique using an XGBoost model trained to detect land and cloudy pixels over water. The workflow incorporates depth correction using Lyzenga’s algorithm and superpixel analysis, culminating in an unsupervised classification of reef areas using KMeans. Results demonstrate the effectiveness of this approach in producing consistent, interpretable classifications of reef ecosystems across different imaging conditions. This study highlights the potential for scalable, autonomous monitoring of coral reefs, offering valuable insights for conservation efforts and climate change impact assessment in shallow marine environments.