Bio-assessment protocols for the subsurface domain of river channels (i.e. hyporheic zone) are scarce despite of the known importance of its ecological function in river ecosystems. The larvae of the Alloperla ishikariana Plecoptera species inhabit the hyporheic zone. Therefore, we examined whether emergent adult A. ishikariana could serve as proxy indicators of the effects of pollution in the hyporheic food web. The study site comprised a 15-km stretch of a gravel bed river in Hokkaido, Japan, from which all invertebrates were collected from the riverbed at a depth of 30–50 cm, and emergent A. ishikariana adults were sampled in riparian zones. Water quality changed gradually along the river owing to the effects of a wastewater treatment plant and surrounding land uses. Nitrogen and carbon stable isotope ratios (SIRs) of epilithic biofilms, hyporheic particulate organic matter (POM), benthic POM, and invertebrates were used to determine the major basal carbon sources, the effects of water pollution on the hyporheic zone, and the trophic positions of dominant invertebrates. Generalized linear (mixed) models were used for statistical testing and modeling. Amphipoda and the larvae of A. ishikariana were considered as top predators and secondary consumers in the hyporheic food web, respectively. The observed similarity in water quality between the hyporheic and surface water suggested a large degree of hydrological exchange between the two zones, and resulted in positive increases in the nitrogen SIRs of hyporheic invertebrates, including A. ishikariana larvae, in proportion to nitrate levels in the surface water. The nitrogen SIRs of A. ishikariana adults were significantly correlated with the nitrogen SIRs of their larvae within the same location (adjusted R² = 0.78), indicating that emerged adults can provide information on the longitudinal variability of the effects of synthetic nitrogen. In contrast, the carbon SIRs of adults did not predict those of their larvae, possibly reflecting the diverse feeding habitats of larvae. Overall, we demonstrated that adult aquatic insects emerging from the hyporheic zone can be used as indirect indicators of pollution-associated nutrient assimilation as well as the spatial heterogeneity of dietary carbon resources in hyporheic food web.