Long-term monitoring studies are needed to understand changes in ecosystem status when restoration measures are implemented. A long-term data series (1996–2007) of the Tagus estuary (Portugal) intertidal and subtidal benthic communities was collected in a degraded area where mitigation measures were implemented. Multivariate analysis was used to analyze spatial and temporal patterns in benthic community composition and trends in five benthic community metrics (i.e., taxonomic richness, density, biomass, Shannon–Wiener diversity and the AMBI index) were also examined. The results revealed a clear separation between intertidal and subtidal assemblages, although they had 50% of taxa in common, including the most abundant. Significant positive trends were found for all metrics showing that both intertidal and subtidal communities responded to the restoration measures implemented. Nevertheless, biotic indices need some adaptation before being universally applied to intertidal and subtidal habitats.