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Abstract Glucocorticoids (corticosterone/cortisol; cort) are frequently used in conservation as biomarkers of disturbance in wild populations. However, the context‐dependent nature of cort means that it may not always accurately reflect disturbance. For example, there is growing evidence that wildlife populations can evolve or acclimate to human‐induced environmental change (i.e. contaminants) by expressing higher levels of tolerance. Mechanisms that allow for populations to achieve higher contaminant tolerance can be related to cort and thereby impact the reliability of cort as an indicator of disturbance. This study asks: (1) do wildlife populations that differ in tolerance to contaminants differentially express baseline and stress‐induced cort and (2) is cort a viable indicator of disturbance across populations that differ in tolerance to contaminants? Toward this goal, we identified three wood frogRana sylvaticapopulations with relatively high NaCl tolerance and three populations with relatively low NaCl tolerance. Tadpoles from these populations were reared to metamorphosis in either an environmentally relevant concentration of NaCl (0.5 g L⁻¹NaCl) or a control (0 g L⁻¹NaCl). At metamorphosis we used a non‐invasive waterborne assay to measure baseline and stress‐induced cort release rates and measured fitness‐related metrics. We found that contaminant tolerance influences cort levels. More tolerant populations had lower baseline cort and higher fitness compared to less tolerant populations. However, despite variation in cort across populations with different levels of tolerance, cort still represents a viable indicator of condition as our results show a consistent negative relationship between cort and fitness. Lastly, we found that levels of cort were consistent regardless of whether amphibians were reared in NaCl contaminated or non‐contaminated environments. Overall, we emphasize the importance of recognizing population‐level variation in cort due to contaminant tolerance when using cort as a biomarker for conservation purposes.