Food web studies have provided insight into the dynamics of benthic ecosystems and their stability, stimulating research into the importance of different organic matters (OM) inputs in the ecological and metabolic processes that affect community structure. Using stable isotope analysis (SIA) and Bayesian ellipses, this study examines the influence of terrestrial OM and hydrographic conditions on food web structure and niche width in a glacial system (Baker/Martínez fjord complex). Two ecological groups were identified; one located in the inner and middle fjord and the other one in the outer fjord. Both had isotopically less diverse feeding groups in comparison to non-glacier benthic communities, comprising four trophic levels. In addition, the study area exhibited high trophic redundancy (e.g., species with overlapping trophic niches) associated with chronic natural physical disturbances from glacial sedimentations, which have shaped this non-selective feeding benthic community. The trophic structure metrics suggest that the benthic food web is supported principally by primary production and terrestrial OM pathways, but macroalgal subsidies could be important to detritivores via floating kelp in the inner area of the fjord. The results of this study suggest that glaciofluvial benthic communities have higher trophic redundancy associated with environmental disturbance conducted by sediment load, shaping a benthic community with a lower alpha diversity and fewer trophic levels in comparison to no-glacier environments.