The accurate estimation of trophic discrimination factors (TDFs) for stable carbon and nitrogen isotopes (Δ13C and Δ15N) requires studies for each particular species or taxonomic group, because the use of general TDFs values for all animals obtained from the literature represents an important bias in isotopic modelling. Values for Δ13C and Δ15N were estimated in an aquatic food chain (periphyton-Chironomini-Perithemis sp.), in a subtropical region of South America, under experimental conditions using two approaches: i) Traditional arithmetic equation and ii) Bayesian inference from mixing models. The effect of diet quality on TDF variability was also evaluated. We report values for Δ13C and Δ15N for Chironomini when feeding on periphyton (1.12 ± 1.31‰ and 0.92 ± 1.94‰ for C and N, respectively using the arithmetic equation) and for Perithemis sp. when feeding on Chironomini (0.65 ± 1.52‰ and 0.90 ± 1.08‰ for C and N, respectively, according to the arithmetic equation). We obtained similar results when using Bayesian inference. We did not find effects of diet quality on Δ13C and Δ15N values; although we highlighted that, unexpectedly, the taxonomic composition of periphyton strongly affected the isotopic values of C and N. These reported values improve the accuracy of isotopic modeling for subtropical aquatic macroinvertebrates in future food web research.