The benthic community in the Chilean Patagonia is as rich and highly diverse as the spatial variation of its habitats and food sources. Environmental stress from glacier melt and river discharge are known drivers of benthic community dynamics. Here, we analyze longitudinal patterns of soft-bottom benthic communities across transects of glacier-marine environments and how these habitats may respond to changes in the environmental conditions. To assess the relationships between environmental heterogeneity (marine and glacial habitats) and benthic biodiversity, this paper reviews biological (mega- and macroinfauna) and sedimentological dataset from multiple oceanographic campaigns in Chilean Patagonian fjords. Furthermore, we analyze isotopic compositions of epibenthic and macroinfaunal organisms (δ13C/δ15N and C/N) to determine particulate organic carbon (POC) and particulate organic nitrogen (PON) availability and organismal stoichiometric budgets within each benthic community. Our results showed that glaciomarine and glaciofluvial environmental stress negatively affected nutrient reservoirs and organic matter (OM) availability, and hence produced changes in benthic diversity and trophic structure throughout the fjords. These conditions shaped the benthic community where small-bodied polychaetes and opportunistic species dominated. Additionally, we found a strong relationship between OM and nutrient availability with faunal isotopic composition, but a decoupling in C/N ratios between fauna and sediment OM, suggesting preferential organic carbon use under limited nitrogen in fjord sediments.