Benthic organisms are considered among the best bioindicators being closely associated to sediments in which many pollutants are stored. In this study, macrophytes and meiofauna have been investigated in a transitional area (Venice lagoon, Italy) characterized by numerous anthropogenic pressures. Macrophyte Quality Index and meiofaunal richness were used to assess Ecological Quality (EcoQ) status in line with Water Framework and Marine Strategy Framework Directives. Comparing the EcoQ classes, the results appeared consistent in 24 sites, whereas, in the remaining 5 ones, the values significantly diverged. These results could be related i) to the presence of the seagrass Cymodocea nodosa that could affect meiofaunal taxa with the production of tannins; ii) to the different time response of these communities to human impacts. This synergistic investigation has allowed an accurate description of the spatial and temporal changes of meiofauna through data on abiotic and biotic parameters characterizing the ecosystem trophic level.