In the context of the limited information on the ecology of port communities, the present work aims at assessing the small-scale spatial variability of zoobenthos inhabiting hard and soft substrata, in a Mediterranean port with high levels of commercial shipment. Samples were collected in summer from three stations and four depth levels, using core and quadrate samplers. A total of 34,578 individuals were collected, identified to 118 animal species. Soft substratum communities were impoverished and their structure varied spatially according to sediment composition. At a functional level deposit feeders dominated; their abundance decreased at the silty sites. Biotic indices were found inadequate for the assessment of ecological quality, due to the very low abundance of the fauna. Fouling communities varied spatially in vertical scales; diversity indices and the abundance of Bivalvia varied also in horizontal scales. Suspension and deposit feeders dominated showing a decreasing trend with depth. Two animal-dominated communities, serpulid blocks in the lower midlittoral zone and mussel beds in the sublittoral, substituted an algal-dominated community, which has been previously recorded from the same port quays. This substitution may be due to the intensive mussel farming in the nearby area contributing to the rapid expansion of mussels and of their serpulid biofoulers. Despite the existence of biogenic substrata, which enhance habitat complexity, the diversity of the associated fauna decreased and most species were tolerant to organic pollution. Recursive biomonitoring seems necessary to assess the ecological status of communities and to develop integrated management plans for temperate ports.