A method of ocean color data processing using the combined near-infrared (NIR) and shortwave infrared (SWIR) bands for atmospheric correction for the Moderate Resolution Imaging Spectroradiometer (MODIS) on Aqua is proposed. MODIS-Aqua has been producing the high quality ocean color products in the open oceans, but there are still some significant errors in the derived products in the coastal regions. With the proposed NIR-SWIR combined algorithm, MODIS ocean color data can be processed using the standard (NIR) atmospheric correction algorithm for the open oceans, whereas for the turbid waters in the coastal region the SWIR atmospheric correction algorithm can be executed. The turbid water index developed by Shi and Wang (2007) (Remote Sens. Environ. 110, 149-161 (2007)) is computed prior to the atmospheric correction for the identification of the productive and/or turbid waters where the SWIR algorithm can be operated. For non-turbid ocean waters (discriminated using the turbid water index criterion), the MODIS data are still processed using the standard (NIR) algorithm. The NIR-SWIR combined algorithm has been tested and evaluated. Two examples from MODIS-Aqua measurements along the U.S. and China east coast regions show improved ocean color products with the new approach. In particular, there are no obvious data discontinuities between using the NIR and SWIR methods. Therefore, with the NIR-SWIR combined approach for the MODIS ocean color data processing, good quality ocean color products can be derived both in clear (open) oceans as well as for turbid coastal waters.