In order to better understand environmental disturbances in the French coastal Mediterranean lagoons, we used an ecotoxicological approach based on the measurement of the toxicity of the sediments using oyster embryo bioassay that provides a basis for assessing the effects on the fauna of contaminants adsorbed on the sedimentary particles. The study covers all of the main lagoons of the French Mediterranean coasts of Languedoc Roussillon, Camargue, and Provence (Berre and Bolmon lagoons), where 188 stations were sampled. The toxicity tests provide evidence of variable levels of toxicity in sediments. Contaminated lagoons such as La peyrade, Le canet, and Ingrill and locally affected lagoons such as Bages-Sigean, Vaccares, Bolmon, and Berre have sampling stations with 100% of larval abnormalities during 24-h development. In all of the lagoons, the toxicity was mainly located close to local harbors and rivers. Salses Leucate (Languedoc roussillon) lagoon was found very clean, with no important toxicity. The results are discussed in terms of environmental disturbances of the coastal lagoons and with regard to the long-term monitoring of the impact of contaminants on the coastal environment.