For parasites with complex life cycles, the ecological traits determining host competence and seasonal changes in infection in natural habitats are often unclear, making it difficult to predict infection dynamics, including disease outbreaks. Hairworms (phylum Nematomorpha) require both aquatic and terrestrial hosts to complete their life cycle. Although hairworm host competencies have been tested in laboratory experiments, knowledge of the paratenic hosts (aquatic insect larvae) in their natural habitats is limited. This study clarified the species of aquatic insect larvae that are primarily infected by hairworms as paratenic hosts over a year in a mountain stream in central Honshu, Japan. The monthly prevalence and mean abundance of hairworm cysts were high in Ephemera japonica larvae (Ephemeridae: Ephemeroptera) throughout the study period (20.0–88.9 and 0.2–36.8%, respectively). These high prevalence and abundance values may be attributable to their filter-feeding behavior as well as their depositional habitat use. The hairworms also infected leptophlebiids (Ephemeroptera; scrapers), the perlid Calineulia sp., the chloroperlid Haploperla japonica (Plecoptera; predators), and chironomids (Diptera; filter-feeders or predators). The abundance of the cysts tended to be high in aquatic insects inhabiting pools rather than riffles, and the seasonality reflects the reproductive season of the hairworms as well as the phenology of their paratenic hosts. Filter-feeding ephemeropterans inhabiting pools were the major paratenic host of the hairworms in our study site, although their universality and effectiveness as the transporter to definitive hosts remain unclear.