Using stable carbon and nitrogen isotope analysis (δ13C and δ15N) to assess trophic interactions in freshwater ecosystems is a well established method, providing insight into ecosystem functioning. However, the spatial and temporal variability of isotope values, driven by environmental fuctuation is poorly understood and can complicate interpretations. We investigated how the temporal variation of stable isotopes in consumers (fsh, crayfsh and macrozoobenthos) of a canyon-shaped oligotrophic reservoir is associated with environmental factors such as water temperature, transparency, fooded area, and water quality measures. Consumers and their putative food sources were sampled and analyzed for carbon and nitrogen stable isotopes annually, and environmental parameters were measured monthly from 2014 to 2016. Results revealed signifcant diferences in δ13C and δ15N values in each consumer among studied years. Over the years, fsh and crayfsh expressed diferences in δ13C between 3 and 5‰, whereas in zoobenthos diferences were 12‰. Variability in δ15N was similar across all consumers (2–4‰). Moreover, results suggest that the fooded area of the reservoir was a major driver of δ13C stable isotope values variation in consumers, while variation in δ15N was not linked to any of the studied environmental factors. Bayesian mixing models further showed signifcant changes in the origin of detritivorous zoobenthos carbon sources (reversal shift from terrestrial detritus to algae origin) between years with low water level to years with the standard water level. Other species showed only slight diferences in food source utilization among years. Our study highlights the importance of environmental factors as sources of variation in consumer’s stable isotope values which should be considered especially when studied ecosystem strongly fuctuate in some environmental factor.