Biological quality in a bay affected by man's activities was evaluated by means of the composition of assemblages of sponges and ascidians. Our results showed that the structure of these two groups of filter-feeders aided in discriminating between undisturbed and disturbed areas, establishing different "environmental health categories" from moderately to strongly disturbed areas, and in ascertaining the extension of the area of each "health category". We were able to divide the bay into four zones based on type of disturbance or anthropogenic source: (1) stations free of any source of disturbance, (2) stations under moderate disturbance, located close to industrial ports, millworks, etc., (3) stations that are under the direct influence of industrial wastes such as a power station and oil refinery, and (4) stations near strongly disturbed areas, influenced directly by harmful steelworks activities. We differentiated clearly between four large species assemblages, and related the composition of these assemblages to different kinds of disturbances. Thus, these species could be used to manage the marine environment in this bay by comparing the observed fauna, with expected fauna in an unstressed site. Moreover, the joint presence of the sponge Cliona vastifica and tunicate Policitor adriaticum seems always to indicate a more or less pristine environmental situation, functioning as bioindicators of normal conditions. We think that the use of specific bioindicators for monitoring disturbance is a valid tool to establish baselines to predict impacts associated with industrial development in many marine ecosystems. The advantages to monitoring communities on hard rocks versus sandy or muddy bottoms are also commented upon.