With the ongoing effects of global warming, Antarctic supraglacial meltwater plays a critical role in ice-sheet instability. Spaceborne remote sensing provides a viable solution to detect surface melt in these vast and remote regions. Innovative deep learning image segmentation methods have the potential to improve supraglacial lake (SGL) mapping by adding spatial awareness to the mapping process, as currently established methods only consider the spectral variety of multispectral satellite data (Sentinel-1 and Landsat-8) on a per-pixel basis. In this study, we adapt a U-net image segmentation method to detect SGLs in Sentinel-2 data and quantify its performance in comparison to established mapping approaches in Antarctica. At a 90% probability threshold, the proposed workflow achieves a producer’s accuracy, user’s accuracy, and an F1 score of 0.915, 0.912, and 0.913, respectively. We compare the classification results to those of an established Random Forest classifier, and find that the U-net achieves better results in 13 of the 16 validation scenes. In a relative comparison with five established SGL products, the U-net approach maps, on average, the largest lake area, although there is disagreement between the datasets due to different data sources, cloud cover, and misclassification of some clouds as lakes. The main advantages of the developed approach are its capabilities to map lakes under thin clouds and ice, resulting in more continuous lake areas than conventional approaches, and a reduced number of input features required, which will be advantageous in future large-scale SGL mapping efforts.