The Orbetello lagoon, one of the largest Western Mediterranean lagoons, was affected by high algal blooms and severe anoxic crises in 1992 and 1993, with fish mortality throughout most of the lagoon and a drastic reduction of benthic species. Many measures were undertaken between 1994 and 1996 to remove the severe eutrophication of this lagoon. Such measures included harvesting of the floating seaweed biomass, removal of all wastewater and sea channel enlargement by dredging activity. The aim of the present research was to study the macrozoobenthic assemblage in 1999 and to compare it with previous research in order to assess the recovery of the lagoon. A total of 106 taxa and 45,175 individuals were collected in three areas (sea inlets, western and eastern lagoon) having different organic matter loading during winter and summer. The results of multivariate and correlation analyses indicated that trophic status and its seasonal dynamics were crucial in determining species distribution among the different areas. Moreover, comparison of the macrozoobenthic structure between winter 1995 and 1999 showed differences in species composition and structural parameters in the western and eastern lagoon, where a clear recovery of benthic assemblages was observed in 1999. However, the dominance of opportunistic species in most of the lagoon and the decrease in some structural parameters during summer suggested that this basin still presented signs of disturbance in 1999, six years after the last extended anoxic crises and even after completion of the restoration measures carried out in the environment. It was hypothesized that a secondary disturbance, sustained by a high seasonal release of nutrients from the sediments, could create considerable deviations from the expected improvement in benthic conditions.