Description: We analysed carbon (δ13C) and nitrogen (δ15N) isotope ratios of organisms and biogenic tissues from Comau Fjord (southern Chile) to characterise benthic food webs and spatial isotope variability in this ecosystem. These values were intended to serve as a baseline for detecting anthropogenic impacts on Patagonian marine fjord ecosystems in later studies. Benthic macro algae and invertebrate suspension feeders were primarily considered, with some supplementary data from cyanobacteria, plankton, fish, and coastal vertebrates. Six depth transects typified the lateral salinity gradients from the innermost part of the fjord to its mouth, as well as the vertical density gradients caused by freshwater inflow. Carbon isotope signatures indicated predominant consumption of either CO2 or HCO3– for benthic macroalgal. All CO2 users belonged to rhodophytes. The δ15N values of benthic macrophytes decreased with decreasing salinity, both vertically and along the fjord axis. This implies the influence of 15N-poor terrestrial dissolved inorganic nitrogen (DIN) at these sites. Enhanced influence of freshwater influx also lowered N contents and increased C/N ratios in algal tissues. Exceptionally high macroalgae δ15N values at the seabird and sealion colony Isla Liliguapi point to animal faeces as an additional source of 15N-enriched DIN. Thus, DIN sources not originating from the open sea are additionally utilised by the benthic macroalgae in the fjord. In contrast, mussel tissue from the same locations was much less influenced by varying DIN sources. Among benthic suspension feeders, mytilids (Mytilus chilensis, Aulacomya ater) had the lowest and scleractinian corals (Desmophyllum dianthus) had the highest δ15N values, and Balanidae (Elminius kingii) and gorgonians (Primnoella sp.) showed values in between. The preference for specific size classes of marine particulate organic matter (seston) as food serves as an explanation for the δ15N variability observed between the different benthic suspension feeders.