Benthic communities were studied twice (during the autumn and spring) in three Mediterranean coastal lagoons located in Greece (Logarou) and Italy (Cesine and Grado-Marano). The species composition and distribution, community diversity, species richness, dominant taxa and their ecological identity, benthic trophic and biomass size structure were investigated in these lagoons and the results were correlated with the environmental variables. The overall similarity based on species composition and abundance among the lagoons was low due to the differences in the dominant environmental factors, whereas the variations in the community diversity and species richness were mainly related to the degree of marine influence, reflecting the natural structure. The benthic classification indices AMBI, M-AMBI, BENTIX, BO2A, ISD and ISS were applied to assess the ecological status of the lagoons studied. The results revealed that the biotic indices AMBI, M-AMBI, BENTIX, and BO2A were not adequately efficient due to the natural dominance of the tolerant and opportunistic species and the correlation of the species diversity with natural stress. The ISD and ISS, on the other hand, based on size distribution frequencies and on size spectra sensitivity, respectively, showed good discrimination power among the impacted and unimpacted sites. The results indicate that except for species sensitivity, other traits of the communities such as the biomass or size structure could be more robust, sensitive and suitable for assessing the ecological quality of lagoons.