The Thau lagoon, located in southern France, suffers episodically from anoxic crises locally known as 'malaigue'. Such crises mostly occur under warm conditions, low winds leading to a strong eutrophication of the lagoon. The development of a sulphur bacterium sometimes gives locally to the waters a 'milky turquoise' appearance and leads to shellfish mortality. One of the indicators of the eutrophication status of the lagoon can be surveyed by the chlorophyll product provided by remote sensing images such as Medium Resolution Imaging Spectrometer (MERIS). In this paper we compare chl2 (or algal2) estimations provided by MERIS level 2 products and the ground measurements of chlorophyll a concentrations in water and we propose a linear correction of the chl2 MERIS product. The corrected chl2 estimations obtained over four years are analysed to understand the seasonal evolution of the trophic status of the Thau lagoon. We also study the influence of the anoxic crises of summers 2003 and 2006 on the chl2 estimations and we find a strong correlation between chl2 and the oxygen percentage at 1 m depth (0.70 for measurements in summers 2003 and 2006).