Due to increased anthropogenic pressures on many fish populations, supplementing wild populations with captive‐raised individuals has become an increasingly common management practice. Stocking programs can be controversial due to uncertainty about the long‐term fitness effects of genetic introgression on wild populations. In particular, introgression between hatchery and wild individuals can cause declines in wild population fitness, resiliency, and adaptive potential, and contribute to local population extirpation. However, low survival and fitness of captive‐raised individuals can minimize the long‐term genetic consequences of stocking in wild populations, and to date the prevalence of introgression in actively stocked ecosystems has not been rigorously evaluated. We quantified the extent of introgression in 30 populations of wild brook trout (Salvelinus fontinalis) in a Pennsylvania watershed, and examined the correlation between introgression and 11 environmental covariates. Genetic assignment tests were used to determine the origin (wild vs. captive‐raised) for 1742 wild‐caught and 300 hatchery brook trout. To avoid assignment biases, individuals were assigned to two simulated populations that represented the average allele frequencies in wild and hatchery groups. Fish with intermediate probabilities of wild ancestry were classified as introgressed, with threshold values determined through simulation. Even with reoccurring stocking at most sites, over 93% of wild‐caught individuals probabilistically assigned to wild origin, and only 5.6% of wild‐caught fish assigned to introgressed. Models examining environmental drivers of introgression explained less than 3% of the among‐population variability, and all estimated effects were highly uncertain. This was not surprising given overall low introgression observed in this study. Our results suggest that introgression of hatchery‐derived genotypes can occur at low rates, even in actively stocked ecosystems and across a range of habitats. However, a cautious approach to stocking may still be warranted, as the potential effects of stocking on wild population fitness and the mechanisms limiting introgression are not known.