Substrate, flow type, nutrients, aquatic vegetation, organic matter, and caddisfly community structure were studied at two low order streams (Glyn and Nant y Fall) subjected to pastoral use in the Patagonian mountains. At both sites, we examined the effect of habitat type (boulder-pebble with and without filamentous algae, cobble-pebble, gravel-sand, leaf-pack, the submerged macrophytes Myriophyllum quitense and Isoetes savatieri) and season (high and low water period) on caddisfly assemblages. Benthic particulate organic matter (BPOM) ranged between 4.6 and 472 g m -2 , all allochtonous detrital fractions were significantly higher at leaf-packs at Glyn, whereas M. quitense habitats supported more BPOM and macrophytes biomass at Nant y Fall. As expected, boulder-pebble sustained higher Trichoptera richness than M. quitense and gravel-sand, moreover all habitats showed higher density than M. quitense at Nant y Fall. According to our results at least nine caddisfly species exhibited some habitat preference with boulder-pebble and cobble-pebble the most selected habitat. These particular habitats sustained more than 68% of the total caddisfly species. Multidimensional scaling ordination highlighted differences in composition per habitat for both sites showing a clear distinction among depositional and erosional habitats. Substrate, flow type, detritus biomass were important predictors defining assemblages. Based upon our findings, those anthropogenic actions or stressors that change hydraulic as well substrate attributes in mountain streams such as stock trampling, dredging, clearing of riparian areas, will reduce caddisfly richness. These results are relevant for outline management and conservation biomonitoring and schemes in headwater Patagonian streams as well as other similar environments worldwide.