This study concerns the spectral behavior of remote sensing reflectance R rs of Thau lagoon water during the anoxic crisis in the summer of 2003 and 2006. The proliferation of photosynthetic sulfur-oxidizing bacteria (SOB) in anoxic water make the water color becomes opaque and turbid until milky. An identification method using 665 nm, 709 nm and 754 nm bands of Medium Resolution Imaging Spectrometer (MERIS) sensor is proposed to identify the total anoxic water filled by SOB. The reflectance of the SOB layer is described as a specific reflectance relating to the SOB concentration. The results show that SOB contaminated water during the anoxic crisis can be quantitatively remote sensed by multispectral sensor.