The effects of polarization, sea water salinity, and temperature on top of atmosphere radiances and water leaving radiances (WLRs) are discussed using radiative transfer simulations for MEdium resolution imaging spectrometer (MERIS) channels from 412 to 900 nm. A coupled system of an aerosol-free atmosphere and an ocean bulk containing chlorophyll and colored dissolved organic matter (CDOM) (case 1 waters) was simulated. A simple, but realistic, bio-optical model was set up to relate chlorophyll concentration and wavelength to scattering matrices and absorption coefficients for chlorophyll and colored CDOM. The model of the optical properties of the sea water accounts for the salinity, temperature, and wavelength dependence of the relative refractive index, as well as the absorption and the bulk scattering coefficient. The results show that the relative difference of WLRs at zenith for a salinity of 5 practical salinity units (PSUs) and 35 PSU can reach values of 16% in the 412 nm channel, decreasing to 4% in the 900 nm channel. For the more realistic case of 25 PSU compared to 35 PSU, the effect is reduced to 5% for the 412 nm channel and decreasing to 2% for the 900 nm channel. The effect on radiance caused by changing sea water temperature is dominated by changes of sea water absorption and shows strong spectral features. For WLRs, a change of 10°C can cause relative changes of above 3%. The effects of neglecting polarization in the radiative transfer depends strongly on direction and wavelength, and can reach values of ±8% for the 412 nm channel. The effect is discussed for MERIS channels, viewing geometry, and chlorophyll content.