The consequences of a sudden decrease in water salinity on a macrophyte community dominated by the marine species Zostera noltii were investigated in a shallow coastal lagoon (Southern France). The expected change in the community assemblage was a competitive displacement of Z. noltii by Potamogeton pectinatus and Ruppia cirrhosa. However, the results of an eight-year survey did not validate this hypothesis. Zostera noltii remained dominant after three years at low salinity (ca. 5) and then suddenly disappeared within one year. The decline of Z. noltii was not associated with an increase of other species. The maximum depth colonized by all species decreased, suggesting that light availability became a limiting factor for the aquatic vegetation. The high concentration in suspended sediments that was measured when salinity was low may result from the synergetic effects of low salinity that slowed down the settling of suspended sediments and the disappearance of Z. noltii meadow that trapped sediments and reduced wave energy. The progressive recovery of the Z. noltii meadow following the increase in water salinity was associated with an increase in depth limit of the other species. However, the two other angiosperms remained present at low frequency of occurrence and the two charophytes (Lamprothamnium papulosum and Chara galioides) declined over the study period. A geo-referenced database was constructed to investigate the spatial variation in Zostera noltii cover in relation to depth, slope, wave exposure and sediment characteristics using logistic regressions. During the first years of re-colonization, when Z. noltii was restricted to the shallow borders of the lagoon with the highest slope values, the best explanatory variables were depth and slope. In the following years, depth and wave exposure were the most important factors determining the spatial distribution of Z. noltii. (c) 2005 Elsevier Ltd. All rights reserved.