Accurately mapping surface freshwater bodies (e.g., ponds, reservoirs, and small lakes) is vital for managing insular ecosystems and communities. However, satellite-based extraction in coastal settings is challenged by seawater intrusion, complex topography, and cloud cover. Focusing on bedrock islands outside China’s Pearl River Estuary, this study developed a robust method to address these issues. We used both Gaofen-1 (GF-1) optical and Gaofen-3 (GF-3) Synthetic Aperture Radar (SAR) imagery, supported by field-collected water quality samples from surface freshwater body shorelines for model training and validation. The performance of two index-based methods (the Normalized Difference Water Index, NDWI, and the Normalized Difference Vegetation Index, NDVI), two machine learning algorithms (Random Forest, RF, and Support Vector Machine, SVM), and a U-Net convolutional neural network (U-Net) deep learning model was compared. The U-Net model achieved the highest accuracy, with Area Under the Curve (AUC) values of 0.881 (GF-1) and 0.840 (GF-3). It effectively discriminated freshwater from seawater and mitigated cloud interference, demonstrating superior precision and robustness over traditional methods. This work establishes a high-precision framework for monitoring island freshwater resources, supporting sustainable water management. The proposed framework provides a practical tool for tracking freshwater availability under climate variability and anthropogenic pressures, contributing to the monitoring of Sustainable Development Goal (SDG) indicator 6.3.2 on ambient water quality.