An atmospheric correction algorithm based on zero water leaving reflectance in short wave infrared (SWIR) bands for case Ⅱ waters was presented. It used two SWIR bands of MODIS(1.240μm and 1.640μm) to extrapolate the aerosol scattering reflectances of visible and near infrared ( NIR ) bands. Then water leaving reflectances in visible and NIR bands could be retrieved. This algorithm was tested over coastal waters and lakes in the east part of China. The correc- tion results were compared with both in situ measurement data and those by other atmospheric correction algorithms. The results show that the algorithm removes the effects of atmosphere effectively.