An energy budget provides a useful tool for examining the exchange of energy between trophic levels. In this study we examined the potential for autotrophic productivity and organic material to support higher trophic levels in three distinct geomorphic segments of the Kootenai River, USA. This approach is particularly important given that several species of fi sh, including the endangered Kootenai white sturgeon (Acipenser transmontanus), have been in decline since the installation of a large hydropower and fl ood control dam on the river. Previous research indicated that (i) the reservoir formed by Libby Dam was retaining signifi cant quantities of nutrients and organic material and (ii) phosphorus was limiting periphyton accrual downstream from the reservoir. Thus food limitation was a likely mechanism contributing to the decline in fi sh populations. Net daily metabolism (NDM) was positive during only 30 % of the growing seasons from 1993 to 1995 indicating that autochthonous production was rarely suffi cient to support higher trophic levels. All reaches were generally exporting transported organic matter (TOM). Results of an energy budget indicated that macroinvertebrate standing crop was generally lower than that which could be sustained by the relatively short bursts of positive NDM. Estimated fi sh biomass was higher than that sustained by positive NDM or stored TOM at energetic conversion effi ciencies (C.E.) of 10 % at average and maximum estimated active metabolic rate. Autotrophic and detrital sources were generally insuffi cient to support the estimated fi sh biomass. This study combines detailed analyses of both the autotrophic and detrital energy pathways and thereby suggests a mechanistic explanation for the decline in fi sh abundance ultimately caused by impoundment.