Around 90% of the oceanic and inland waters’ reflectance registered in satellite detectors comes from the atmospheric contribution. Hence the water-leaving radiances in the Near-InfraRed (NIR) region are above the zero value over inland waters because of sediments and dissolved organic particles, this radiance cannot be ignored. To accurately retrieve water quality parameters from water-leaving reflectance, atmospheric correction is the most important step. This study evaluated five reliable atmospheric correction algorithms (AC) known as: (ACOLITE, C2RCC, iCOR, 6SV, and Sen2Cor) against optical in-situ measurements collected above the water in Qiandao Lake, China using Sentinel-2 Multi-Spectral Imager. 60 in-situ water samples and optical measurements (range 400–900 nm) above the water were collected at different points in Qiandao Lake. The spectra measurements were used to validate the atmospheric correction processors. All ACs that were evaluated showed high levels of uncertainty. ACOLITE and ICOR performed the best statistics with root mean square differences (RMSD) (0.006 sr⁻¹) while Sen2Cor achieved the lowest RMSD (0.023 sr⁻¹) across the different modules. ACOLITE, had a better performance when applied to meso- and hypereutrophic waters, compared with oligotrophic, while C2RCC performs better at the wavelength of 833 nm (0.007 sr⁻¹). Finally, 6S performs better at the wavelength of 665 nm (0.015 sr⁻¹). This study introduces insights and addresses a significant research gap in the field of atmospheric correction for satellite imagery over inland waters. Prior studies have primarily focused on atmospheric correction algorithms for coastal and open ocean environments while few studies focused on the unique characteristics and challenges associated with inland water bodies. The findings of this study are crucial for researchers, remote sensing experts, and environmental scientists working with Sentinel-2A imagery, as it enables them to make more accurate and reliable interpretations of water quality and other environmental parameters derived from satellite data.