We investigated the impact of fish farming on the benthic biota of 2 habitats (sea-grass meadows of Posidonia oceanica and non-vegetated soft bottoms), by examining in detail the nematode assemblages, and the effects of organic enrichment on their abundance, diversity (species richness and trophic diversity), community structure and individual size. All investigated faunal variables differed significantly between impact and control sediments, except for individual nematode biomass. Nematodes displayed reduced biodiversity beneath the investigated fish farms in both vegetated and non-vegetated habitats. The nematode genera Richtersia, Desmoscolex and Halalaimus were highly sensitive to biodeposition and disappeared almost completely in farm sediments, whereas other genera such as Daptonema and Prochromadorella largely increased their relative abundance. The impact of biodeposition was investigated also in terms of K-dominance curves and functional variables (life strategies as maturity index, and functional [i.e. trophic] diversity) which showed that nematodes are very sensitive to this kind of environmental disturbance. Our results indicate that the analysis of nematode assemblage composition, the life traits of the dominant species and the presence/disappearance of certain nematode species represent a reliable tool for monitoring the quality state of marine sediments exposed to fish-farm organic wastes.