Resource availability influences the flow of energy through food webs, thus affecting biomass and trophic structure of consumer communities. To assess the effect of availability of allochthonous (leaf litter) and autochthonous (periphyton) resources on the trophic structure of macroinvertebrates, we sampled monthly for a year two sites (upstream forested, downstream open canopy) of Challhuaco, a low order mountain stream in the Patagonian Andes. Leaf litter and periphyton dynamics showed the expected pattern, peaking in autumn and spring, respectively. Temporal variations of shredders and scrapers were synchronized, with the logic delay, with resource abundance. Although leaf litter mass was similar at both stream reaches, shredders were more abundant at the forest site. Periphyton biomass was higher at the forest, while scrapers were more abundant at the open site. The patterns of resource and consumer abundance, and community functional structure were mostly explained by the interaction of abiotic factors and trophic relationships.