To assess the recovery of the lagoon in the Valle di Gorino, Italy, the macrobenthic assemblages were studied throughout a two year period, i.e. before and after the opening of a floodgate. Three stations were located along a gradient of confinement, and sampled for macrofauna, water and sedimentary parameters. Analyses were performed through univariate and multivariate techniques. The macrobenthic assemblages were characterized by a small total number of species, strong dominance in number by a few of these species, and low diversity, but changes in community structure and composition were clearly recognizable. Significant negative correlations were found between macroalgae and macrobenthic community attributes. The altered hydrological regime due to the opening of the floodgate disrupted macroalgal cycles and altered the related macrofaunal successional dynamics: species linked to the macroalgal degradation phase became dominant throughout the Valle. After the intervention, all areas exhibited similar species composition and abundances, and appeared to be in a permanently disturbed condition. A rescaling of environmental conditions repositioned species roles in the community: those species which were typical of a certain phase of the former successional progression, were successively dominating the whole lagoon, irrespective of time and the estuarine gradient. After the intervention, the spatial and temporal distribution of macrobenthic taxa was under the control of factors linked to organic enrichment of the sediments.