The present study investigates the different uses and the functional roles of shallow habitats for fish fauna in the Venice Lagoon, by applying the functional guilds approach. Temporal (seasons) and spatial (location) changes within the lagoon show different habitat uses by fish assemblages, not influenced by local factors. Unvegetated mud habitats (salt marsh creeks and sub-tidal mud flats) and sparsely vegetated (seagrass) habitats show a common nursery role, especially for marine migrant fishes; but, contrary to other similar areas elsewhere shallow seagrass beds in the Venice Lagoon do not have a primary nursery role. This latter habitat has a more important role as a spawning ground for a resident, highly specialized component of the fish community. The habitat uses and their role to fish fauna illustrate the balance between predation risk and foraging profitability, as major factors structuring the fish assemblages. Spatial effects at a larger scale also highlight general characteristics of the fish assemblages in the Venice Lagoon. These indicate differences between the Northern sub-basin and the other two lagoon sub-basins, due to differences in the hydrodynamic regime, habitats distribution, and contributions from land and sea. (c) 2005 Published by Elsevier Ltd.