V. parahaemolyticus, V. vulnificus and V. cholerae non-O1/non-O139 are present in coastal lagoons of Southern France. In these Mediterranean regions, the rivers have long low flow periods followed by short-duration or flash floods during and after heavy intense rainstorms, particularly at the end of the summer and in autumn. These floods bring large volumes of freshwater into the lagoons, reducing their salinity. Water temperatures recorded during sampling (15°C to 24°C) were favorable for presence and multiplication of vibrios. In autumn 2011, before heavy rainfalls and flash floods, salinities ranged from 31.4‰ to 36.1‰ and concentrations of V. parahaemolyticus, V. vulnificus, and V. cholerae varied from 0 to 1.5 X 103 MPN (Most Probable Number)/L, 0.7 to 2.1 X 103 MPN/L, and 0 to 93 MPN/L, respectively. Following heavy rainstorms that generated severe flash flooding and heavy discharge of freshwater, salinity decreased, reaching 2.2‰ to 16.4‰, within 15 days, depending on the site, with a concomitant increase in Vibrio concentration to ca. 104 MPN/L. Highest concentrations were reached with salinities between 10 and 20‰ for V. parahaemolyticus, 10 and 15‰ for V. vulnificus, and 5 and 12‰ for V. cholerae. Thus, an abrupt decrease in salinity caused by heavy rainfall and major flooding favored growth of human pathogenic Vibrio spp. and their proliferation in the languedocian lagoons. Based on these results, it is recommended that temperature and salinity monitoring be done to predict presence of these Vibrio spp. in shellfish harvesting areas of the lagoons.