1. Marine managers deal predominantly with shallow coastal waters. These are among the most economically valuable, biologically diverse, and endangered marine ecosystems.  2. Major changes in the composition of biological communities in such shallow seas should be cause for alarm. Changes in the benthic subsystem may provide more information than those in the pelagic subsystem because such changes on the seafloor tend to be more long‐term.  3. In the northern Adriatic Sea, soft bottom communities have been subject to a recent series of dramatic mortalities due to oxygen deficiency (accompanied by marine snow events and a series of anthropogenic impacts). The affected areas measure hundreds to thousands of square kilometres.  4. We document this deterioration based on the two major components of soft bottom communities (the endo‐ and epibenthos), specifically on a key endobenthic species (the sea urchin Schizaster canaliferus) and on a characteristic epibenthic filter‐feeding community.  5. The high frequency of disturbances, coupled with lengthy recovery periods, indicate a long‐term destabilization of the entire ecosystem.  6. Coastal managers must be aware of the significance of such ecological shifts; biological data should form the basis for policy‐ and decision‐making processes. ©1996 by John Wiley & Sons, Ltd.