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Ocean color remote sensing is an important tool to monitor water quality and biogeochemical conditions of ocean. Atmospheric correction, which obtains water-leaving radiance from the total radiance measured by satellite-borne or airborne sensors, remains a challenging task for coastal waters due to the complex optical properties of aerosols and ocean waters. In this paper, we report a research algorithm on aerosol and ocean color retrieval with emphasis on coastal waters, which uses coupled atmosphere and ocean radiative transfer model to fit polarized radiance measurements at multiple viewing angles and multiple wavelengths. Ocean optical properties are characterized by a generalized bio-optical model with direct accounting for the absorption and scattering of phytoplankton, colored dissolved organic matter (CDOM) and non-algal particles (NAP). Our retrieval algorithm can accurately determine the water-leaving radiance and aerosol properties for coastal waters, and may be used to improve the atmospheric correction when apply to a hyperspectral ocean color instrument.