Alpine lakes, which include glacial and nonglacial lakes, are widely distributed in high mountain areas and are sensitive to climate and environmental changes. Remote sensing is an effective tool for identifying alpine lakes over large regions, but in the case of small lakes, the complex terrain and extreme weather make their accurate identification extremely challenging. This paper presents an automated method for alpine lake identification developed by leveraging deep learning algorithms and multi-source high-resolution satellite data. The method is able to detect the outlines and types of alpine lakes from high-resolution optical and Synthetic Aperture Radar (SAR) satellite data. In this study, a total of 4584 alpine lakes (including 2795 glacial lakes) were identified in the Eastern Himalayas from Sentinel-1 and Sentinel-2 data acquired during 2016–2020. The average area of the lakes was 0.038 km2, and the average elevation was 4974 m. High accuracy was reported for the dataset for both segmentation (mean Intersection Over Union (MIoU) > 72%) and classification (Overall Accuracy, User’s and Producer’s Accuracies, and F1-Score are all higher than 85%). A higher accuracy was found for the combination of optical and SAR data than relying on single-sourced data, for which the MIoU increased by at least 12%, suggesting that the combination of optical and SAR data is critical for improving the identification of alpine lakes. The deep learning-based method demonstrated a significant improvement over traditional spectral extraction methods.