In 1990 two artificial reefs were deployed in southern Portuguese coastal waters, off Faro (FPR) and Olhão (OPR) respectively. In order to investigate the fish assemblages and their intra-annual variability, the two artificial reefs were monitored monthly by means of visual censuses from March 1994 to February 1995. Due to the complexity of the reefs, three strata were considered for fish counts. The two artificial reefs showed similar patterns in terms of residence status and spatial occupation. Most species recorded are characteristic of the infralittoral, the Sparidae family being the most represented. OPR, which is located closer to the main openings of the Ria Formosa lagoon, showed higher mean values than FPR in terms of: fish density (2.01±0.74 fish/m3), fish biomass (123.6±77.4 g/m3) and number of species (7.5). The effect of the juvenile fish migrations from the lagoon to the coastal waters was more evident at OPR. FPR showed a greater intra-annual variation of the ecological indexes than OPR. The results show that artificial reefs that are equal in terms of complexity and size may aggregate different fish assemblages as a result of their isolation and the influence of both hydrological features (e.g. water temperature) and endogenous biological processes in the area (e.g. proximity of nursery grounds).