Taxonomic and functional trajectories of benthic assemblages were studied in shallow soft-bottom sediments in the bay of Saint-Brieuc (Western English Channel). Changes were assessed at different spatial and temporal scales using a macrobenthic dataset based on 38 stations sampled in 1987 and 2019, coupled with data from one station sampled annually between 2005 and 2019 as part of the European Water Framework Directive monitoring programme. Taxonomic trajectories indicated 1) changes in the structure and distribution of benthic assemblages, 2) an homogenization of the assemblages, and 3) significant functional shifts. Fishing activities and nutrient enrichment are probably strong drivers of the observed changes, as suggested by the higher mortality rate of fragile, flexible, tubiculous and burrowing species, and the increase in the abundance of opportunistic species in the assemblages. Certain populations of macroinvertebrates seem jointly controlled by climate change and by the aforementioned local factors of disturbance. The Community Trajectory Analysis framework appears as a new and interesting method to track ecological changes in marine ecosystems by measuring change with respect to a baseline state, to help define ecological recovery (station returning to the initial ecological state) and departure (station presenting increased changes over time), and to analyse trajectory similarity. According to the degradation of habitat over time, we identify the need for the implementation of knowledge-based conservation strategies, especially within Natura 2000 sites.