AbstractFunctional diversity research enhances our understanding of ecosystems and both their functioning and their responses to environmental variations. This study investigated the biological trait responses of benthic invertebrate communities to various environmental conditions in estuarine habitats. We analyzed benthic macroinvertebrate communities in freshwater and estuarine environments to compare their characteristics between estuary sites with and without artificial barriers. Moreover, we combined taxonomic analyses (species richness, abundance, and four community indices) with functional diversity indices and biological trait analyses. The major results are as follows: (i) the most important environmental factors shaping species distribution in estuarine habitats were salinity and electrical conductivity; (ii) comparing functional diversity indices, tidal estuaries revealed that seawater intrusion induced changes in species distribution and the dispersion of benthic macroinvertebrates; (iii) the presence or absence of artificial barriers in estuaries affected biological traits owing to the influence of specific functional strategies of certain species. Consequently, the presence or absence of artificial barriers in estuaries can lead to significant changes in habitat connectivity and functional diversity related to ecosystem functions. These findings indicate that the presence of artificial barriers can significantly influence the ecological dynamics of estuarine ecosystems, thereby affecting species distribution, functional diversity and habitat connectivity. Understanding these effects contributes to a more comprehensive understanding of ecosystem functionings, as it complements existing taxonomic findings and integrates information about the functional aspects of diverse ecosystems.