To examine variation in trophic pathways and the characteristics of food webs from organic matters to aquatic insects, we used stable isotopes to study an intermittent stream system of the Inukami River, Japan. The aquatic insects, including Glossosoma spp., Chironominae spp., Stenelmis spp., Rhyacophilla nigrocephala, and Hexatoma spp., were characterized by different feeding strategies. The ${delta}^{13}C$ values for these species indicated that Glossosoma spp. graze upon periphyton; Chironominae and Stenelmis spp. mainly feed on benthic particulate organic matter, and R. nigrocephala and Hexatoma spp., which were identified as predators, feed upon Glossosoma, Stenelmis, and/or Chironominae spp. This suggests that the trophic position of consumers at each station may be determined by the trophic position of basal food sources in situ. For trophic pathways, the ${delta}^{13}C$ values for both organic matter and aquatic insects tended to gradually decrease, whilst the ${delta}^{15}N$ values increased from the upper reach to the lower reaches, relative to the physicochemical and geographical conditions. These parameters indirectly influence the flow of energy from organic matter to consumers within food web in an intermittent stream system.