Benthic marine food webs, which recycle organic matter and sustain unique biodiversity, are an important component of estuarine Patagonian fjords; however, these may be heavily influenced by salmon farming activities. Under the above conditions, this study collected several food sources (sediment organic matter, suspended particulate organic matter, macroalgae) and 26 benthic invertebrate species, and analyzed them using a Bayesian mixing model. Briefly, carbon and nitrogen stable isotopes analyses revealed that the highly variable isotopic niche widths respond to food supplies from marine and terrestrial organic matter. In addition, particulate and dissolved waste from salmon farming activities were found to modify isotopic composition ratios in many suspension feeders. Particularly, our results indicate high δ15N values in the sponge Cliona chilensis and the encrusting coral Incrustatus comauensis, which appear to be potential ecological indicators for evaluating stoichiometry imbalances and trace organic pollution sources in fjord environments.