1. Reefs built by the annelid worm Sabellaria alveolata in the Bay of Mont-Saint-Michel (France) are the most extensive intertidal biogenic structures within Europe. Before and after mussel farming extensions, a study designed to provide a biological health index of the Sainte-Anne reef (223 ha) was carried in 2001 and 2007 to serve as an easy-to-use management tool and to ensure endangered reef portions were properly targeted and protected. 2. Coupled physical and biological parameters were included in a spatial Health Status Index (HI). A spatial and temporal mapping survey of the HI showed a continuous deterioration of the reef's state of health, particularly in its central part. This degradation correlates with the colonization of the Pacific oyster Crassostrea gigas and with increasing silt deposits on the reef. 3. A combination of several factors is likely to explain such rapid reef deterioration: (1) an increase in trophic competition between cultivated and wild suspension-feeders that is detrimental to the annelids; (2) a modification in the hydrodynamics and consequently in sedimentary patterns leading to an increase in silt deposition; and most importantly (3) an increase in recreational harvesting of oysters and associated reef trampling, resulting in reef fragmentation. 4. Understanding the parameters that influence the reef dynamics is necessary in order to help efficient and effective management and policy focusing on the conservation status of large biogenic structures. Copyright (C) 2011 John Wiley & Sons, Ltd.