A habitat approach was promoted in the framework of ecological status assessment of transitional waters, assuming the importance of habitat heterogeneity to the overall system status. The approach was applied to the use of fish-based multimetric indices by adapting them to seagrass and marsh habitats in the Venice lagoon, Italy, through selection of appropriate metrics and reference conditions. While for marsh habitats, no clear patterns resulted, the index response for seagrass was consistent with the habitat degradation and loss recorded in the lagoon between 2002 and 2005 and with the higher habitat disturbance in southern and central lagoon sub-basins. The assessment of individual habitats is presented as a first step in the process of evaluating the overall condition of a Mediterranean lagoon environment, which should also take account of the diversity of habitats and their availability within the system to properly define an overall index of ecological status.