Human modification of the environment can result in the fragmentation and isolation of natural populations. If isolated populations are small, they may experience higher probabilities of extirpation from genetic, demographic, and environmental effects. One approach for managing fragmented and isolated populations is facilitated migration in which individuals are moved between habitat fragments. Here we report on a study of a single system in which we followed the genetic and population consequences of facilitated migration. We moved a small number of pupfish (Cyprinodon nevadensis pectoralis) from one small spring into another small spring that had become isolated as a consequence of human modification of surface hydrology. We followed the fate of immigrant, resident, and admixed fish over multiple generations using molecular identification of individuals and mark-recapture methods. The mark-recapture data revealed that survival probabilities for admixed individuals were about 20% greater than those for the original resident fish. Furthermore, there was a steady increase in the proportion of admixed individuals, suggesting that immigrant alleles spread through the population consistent with the estimate of relative fitness. Overall, the results suggest facilitated migration can have restorative effects over the course of very few generations, and these results, in the context of other studies, suggest facilitated migration is likely to be an effective strategy for managing populations that have become isolated as a consequence of human modification of landscapes.