Lepidurus arcticus (the Arctic tadpole shrimp) is a vulnerable keystone species in Arctic and alpine water bodies where its occurrence and population size may influence the viability and life history traits of resident salmonids. Using data from a Norwegian mountain hydropower reservoir, Aursjoen, we illustrate how reduced availability of L. arcticus as prey resulted in the reduced condition, growth and delayed maturation of resident brown trout (Salmo trutta). We further link changes in the relative abundance of L. arcticus as prey to changing reservoir conditions, e.g. water level changes in the spring period, thereby establishing an indirect link between reservoir operation regimes and brown trout population traits. While no evidence for decreased brown trout survival was found, the results indicate that alternative brown trout prey resources, i.e. the small chydorid cladoceran Eurycercus lamellatus, do not appear to have successfully offset the caloric loss from reduced consumption of large-sized L. arcticus. Although the fundamental explanation for the observed L. arcticus collapse remains largely unknown, the present findings provide strong evidence that this vulnerable crustacean species can affect the abundance, viability and life history traits of valued resident salmonid populations in oligotrophic alpine lakes and reservoirs exposed to climate- and hydropower-driven changes in water levels and temperature.