We tested the individual and joint effects of stream order, riverbed morphology (i.e. pool-riffle sequence), and season on the structural (i.e. species composition, density and richness) and functional (i.e. percent ratio of shredders, collectors, scrapers, and predators) properties of caddisfly assemblages in a closely natural headwater system (Börzsöny Mts., North Hungary). Each factor, both individually and in interaction had a significant effect on caddisfly assemblages as shown by MANOVA analyses. To clarify the effects of stream order, riverbed morphology and season on caddisflies, assemblage properties were also separately studied by ANOVAs. Percent ratio of shredders and collectors were strongly affected by all factors, whereas other attributes were not always sensitive to stream order, season and riverbed morphology. In contrast, species compositions of the reaches differing in stream order and riverbed morphology were significantly different. Our findings on the contrasting differences in shredder composition between riffles and pools may suggest that not only riparian vegetation, but also instream habitat features could shape the accumulation and retention of particulate organic matter (in streams with pool-riffle heterogeneity).