AbstractIn freshwater systems, δ13C and δ15N stable isotopes can be used to differentiate between pelagic and littoral energy sources and to quantify trophic position. In these ecosystems, crustacean zooplankton are frequently used to characterize the pelagic baseline. Zooplankton samples are often preserved prior to processing and analysis, which can affect isotopic signatures. Variability in preservation effects across studies make it difficult to determine if and how to correct for preservation effects. Here, we develop a correction factor for ethanol preservation and present a flexible statistical method that can be updated with additional data to increase its applicability. We collected zooplankton from five lakes in Minnesota, USA encompassing wide isotopic ranges (δ13C from −37.23‰ to −23.96‰; δ15N from 3.07‰ to 14.44‰). Changes in zooplankton δ13C and δ15N signatures were quantified using a Bayesian hierarchical model predicting fresh values from ethanol‐preserved values. Ethanol preservation increased δ13C by a factor of 1.158 (95% CI 0.866–1.441) and had a negligible effect on δ15N (slope = 1.077; 95% CI 0.833–1.359). Lake‐specific values did not differ from the overall relationship. K‐fold and leave‐one‐out cross validation tests verified that both models were accurate; RMSE of predicted δ13C = 0.701 and RMSE of predicted δ15N = 0.590. Our correction factors could be applied to other systems in which baseline δ13C and δ15N values fall within the range of our study, and this approach also enables the inclusion of data from additional lakes to estimate new corrections.