Macrobenthic communities of the Beagle Channel (BC), Garibaldi Fjord (GF), and the Shelf off the eastern entrance of the Beagle Channel (S) have been investigated. Seven giant box corer stations from the “FjordFlux” (FF) expedition in 2022 were analyzed and spatial differences in abundance, biomass, species composition and diversity studied. The aim of this study is to assess the current state of benthic communities of the BC, adjacent fjords and channels and identify the environmental factors influencing their distribution. The sediment composition, which varies from very fine sediment in fjords, to coarser sediment towards the Atlantic, had a significant impact on the distribution of different feeding types in 2022. A significant separation between the macrobenthic communities of the GF, BC and S-clusters were found. Due to high sedimentation processes in areas closer to glaciers, the GF community was dominated by small, mud-dwelling polychaetes, whereas higher hydrodynamic stress resulted in a more diverse community in the BC and S. The second goal of the study is to investigate changes in benthic communities of the region due to global warming induced environmental changes. Resampling of multibox corer stations of the “Joint Victor Hensen Campaign'' (VH) in 1994 facilitated the investigation of changes in macrobenthic communities more than a quarter century later. Analysis of temporal data revealed a significant separation of the communities in 1994 and 2022. However, species composition showed a similar pattern in both years, with annelids, molluscs and arthropods dominating the communities in 1994 and 2022. Significantly higher abundances were found in 2022, whereas biomass was significantly less than in 1994. Deposit-feeding polychaetes, such as Capitellidae, Spionidae, Paraonidae and Cirratulidae, and the deposit-feeding bivalve Yoldiella indet. dominated the communities in 2022. The study area is subject to pronounced seasonal variability, particularly in the planktonic system. Due to the different sampling periods, seasonal variation in re-production patterns of macrobenthic organisms may explain the high abundances and dispersion of juvenile mussels, especially Yoldiella specimens, throughout the study area in 2022. In the past 28 years, global warming amplified the retreat of glaciers in the region, which led to an increased input of sediments into the marine system, shifting the benthic system towards dominance of small, better adapted species. It is expected that both seasonal and long-term changes in the region are responsible for the distribution patterns observed in 2022.