In temperate ecosystems, resource availability fluctuates seasonally due to changes in environmental conditions and productivity. Intra‐ and inter‐specific trophic niche overlap under resource limitation is a measure of competitive interactions and influences species coexistence and community dynamics, but patterns of this overlap are influenced by anthropogenic activities. To investigate seasonal trophic niche dynamics of coexisting fish species in a flow‐altered river, we analysed prey resources, stomach content samples and stable isotope signatures of mottled sculpin Cottus bairdii and juvenile brown trout Salmo trutta in the Blue River, Colorado, USA, a high‐elevation oligotrophic river. Prey biomass (i.e. benthic macroinvertebrates) peaked in spring and declined through summer and autumn. Stomach content and stable isotope analysis results showed that diet composition of mottled sculpin and brown trout varied seasonally in response to changes in prey availability. Stomach content analysis results revealed that in autumn, both species exhibited the highest frequency of empty stomachs and expanded population trophic niches due to increased inter‐individual diet variation despite decreased individual trophic niche breadth. Inter‐specific trophic niche overlap was relatively high across all seasons, but the lowest degree of overlap occurred in autumn of both years when prey availability was lowest. Isotopic analysis revealed similar trends to stomach content analysis, of wider isotopic niches and reduced overlap in autumn compared to spring. Our data indicated that seasonal variation affected individual‐ and population‐level trophic niche dynamics and inter‐specific niche overlap between mottled sculpin and brown trout. This trophic segregation under resource limitation may serve as a mechanism that facilitates species coexistence in a flow‐regulated, oligotrophic river.