Reintroduction programs are increasingly implemented to regenerate self-sustaining salmon populations. The extent to which returning adults successfully produce surviving offspring is useful for informing reintroduction efforts but is often unknown, as is the genetic makeup of those offspring. We investigated the patterns of reproductive success (RS) among returning Atlantic salmon reintroduced as juveniles in two tributaries of Lake Champlain, by combining extensive river surveys and a molecular parentage analysis. Tissue samples collected from returning adults and their young-of-the-year (YOY) offspring produced in the wild were genotyped using microsatellite loci. Our results suggest that a low proportion of returning adults produced the small numbers of YOY detected in either tributary (range 9.9–13.7%, or 17 of 124 and 8 of 81 returning adults, respectively) and that 81.6% and 1.2% of YOY assigned to a pair of sampled returning adults. These results demonstrate that adults (of different life history strategies) can successfully reproduce in both of the studied tributaries (Winooski and Boquet Rivers) and that unsampled individuals could have recolonized a given tributary. Nevertheless, a larger number of breeders would need to produce surviving offspring in subsequent years to demographically augment the reintroduced population whilst avoiding short-term issues associated with low genetic diversity and inbreeding. Our results also point to underlying ecological problems that may have reduced RS and potential genetic issues within the hatchery-reared population being used for supplementation. Further adaptive management will be needed to ensure self-sustaining populations in this system.