Sun glint masks real physical properties of water and severely interferes with the acquisition of underwater characteristics. Based on the difference between the glint-contaminated pixel and nearby nonglint pixel, the atmospheric absorption feature which can be used to tune the input parameters of the atmospheric radiative transfer model is obtained, then the atmospheric transmissivity is calculated, and the major factors which influence the degree of glint contamination are discussed in detail. According to the fact that the water-leaving radiance value in near-infrared bands is negligible, the spatial distribution of the glint contamination is solved, the glint is removed, and the non-contaminated image is displayed. It is applied to extract the water-leaving radiance, and the experimental results prove the validity of this algorithm.