The Sentinel-2 Multi-Spectral Instrument (MSI) is characterized by short revisit times (5 days), red-edge spectral bands (665 nm and 705 nm), and a high spatial resolution (10 m), making it highly suitable for monitoring water quality in both inland and coastal waters. Unlike SeaWiFS, which can adjust its viewing angles to minimize sunglint, the Sentinel-2 MSI operates with fixed near-nadir angles, which makes it more susceptible to sunglint. Additionally, the complex optical properties of water pose challenges in accurately determining its water-leaving reflectance. Therefore, we compared the effectiveness of six atmospheric correction (AC) algorithms (POLYMER, MUMM, DSF, C2RCC, BP, and GRS) in correcting sunglint using two typical lakes in Xinjiang, China, as examples. The results indicated that POLYMER achieved the highest overall evaluation score (1.61), followed by MUMM (1.21), while BP exhibited the lowest performance (0.62). Specifically, POLYMER showed robust performance at the 665 nm band with RMSE = 0.0012 sr−1, R2 = 0.74, and MAPE = 30.68%, as well as at the 705 nm band with RMSE = 0.0014 sr−1, R2 = 0.42, and MAPE = 38.44%. At the 443, 490, and 560 nm bands, MUMM showed better performance (RMSE ≤ 0.0026 sr−1, R2 ≥ 0.86, MAPE ≤ 28.20%). In terms of band ratios, POLYMER exhibited the highest accuracy (RMSE ≤ 0.093 and MAPE ≤ 22.2%), particularly for the ratio Rrs(490)/Rrs(560) (R2 = 0.71). In general, POLYMER is the best choice for the sunglint correction of Xinjiang’s clean lakes. This study assessed the capability of different AC algorithms for sunglint correction and enhanced the monitoring capability of MSI data in clean waters.