The spatial variability of seagrass meadows in Arcachon Bay, was studied between 1988 and 2008 using a combination of mapping techniques based on aerial photographs for intertidal dwarf-grass (Zostera noltti) beds and acoustic sonar for permanently submerged eelgrass (Zostera marina) populations. The results show a severe decline over the period for both species, as well as an acceleration of the decline since 2005 for Z. noltii. The total surface regression over the studied period is estimated to be 22.8 km(2) for Z. noltii and 2.7 km(2) for Z. marina, which represent declines of 33 and 74% respectively. Environmental data time series spanning the same period were investigated in order to seek the causes for such a decline. The calculated inter-annual trends for temperature, salinity, nitrate plus nitrite, ammonia, suspended sediment and chlorophyll a did not identify any clear environmental change capable of explaining the observed seagrass regression. For instance, no evident sign of eutrophication was observed over the study period. On the other hand, we suggest that the observed variations of ammonia in the inner part of the lagoon are a symptom of the seagrasses' disappearance and thus, a first sign indicating a change of the Arcachon Bay ecosystem towards more instability and vulnerability. Several hypotheses to explain the observed seagrass decay are proposed. (C) 2010 Elsevier Ltd. All rights reserved.