In the context of the application of WFD, a scientific debate is growing about the applicability of biotic indices in coastal and transitional waters. In the present work, the question about the discriminating power of different biotic indices and the relationships with the structure and functioning of the macrobenthic community in a transitional environment is discussed. A time series of samples collected during the last 70 years in the lagoon of Venice, reflecting different environmental conditions (a sort of 'pristine state' in 1935, the distrophic crisis in 1988 and subsequent modifications in 1990, the invasion by an alien species and the developing of high impacting fishery in 1999) has been used. The comparison of results obtained by applying different biotic indices, such as AMBI, Bentix and BOPA, shows differences in the discriminating power of indices and a general overestimation of environmental conditions. Discrepancies between environmental status as indicated by biotic indices and the structure and functioning of the benthic community have been highlighted.