Benthic communities were studied in four transitional water ecosystems in the Mediterranean, located in Albania (Narta), Greece (Logarou) and Italy (Grado-Marano and Margherita di Savoia), with different degrees of salinity ranges, in order to investigate biodiversity trends across a scale of environmental stress. The intensity of natural stress in the transition zones, from the marine-based to the land-based influence, varied from gradual to sharp. The spatial variability in the physical environment had a stronger effect on species richness than did the temporal fluctuations. The sharper the spatial variations of salinity, the lower the number of species and the diversity level of the system. The differences in intensity of natural instability were also reflected by the presence of different sets of species, with the euryhaline species developing large populations and dominating the more enclosed systems, whereas the marine component of the fauna plays the most important role in increasing the level of benthic diversity.