Mudpuppies (Necturus maculosus) are secretive, fully aquatic salamanders with a range that spans much of the eastern United States and Canada including the Great Lakes region. Although this species was once abundant, there have been widespread declines due to habitat loss and modification, pollution, lampricide use, and overcollection. We compared environmental DNA (eDNA) and trapping surveys conducted from 2014 to 2016 to determine Mudpuppy occupancy along the St. Clair-Detroit River System, where this indicator species could be a gauge for success of ongoing restoration. Mudpuppy eDNA was detected at all sites with positive trapping records, as well as one site where individuals have not been trapped previously. Sites with shoreline restoration had the highest occupancy estimates, whereas deep-water restoration did not affect Mudpuppy occupancy. Additionally, eDNA surveys resulted in higher detection probability than setline and minnow trap survey methods, illustrating the benefit of using eDNA to detect secretive species. This study demonstrates the success of restoration efforts in increasing the occupancy of an indicator species and can be used as a template for other restoration initiatives.