The Pennsylvania Game Commission declared the mine at Canoe Creek a protected area for Indiana bats in 1985 and special gates were fitted over the mine entrances. The mine is the most important hibernation site for Indiana bats in Pennsylvania. Additionally, the largest numbers of little brown and small-footed bats in the state are found here. In all, over 26,000 bats of six different species hibernate in the mine, including 700 endangered Indana bats.

A combination of diverse habitats, constant seasonal food supply, summer roosts, and an ideal hibernation spot make the Canoe Creek site an outstanding location for bats. Efforts to learn more about the region's bats, particularly the Indiana bat, and further improve the habitat at the site continue. The Pennsylvania Game Commission has added roof baffles in both the church and the garage next door to increase the roosting area. They have also built a separate bat "condo" near the church that provides extra space for overflow bats, and an alternative roost in the event of a catastrophe at the church.

Telemetry studies are conducted to learn more about foraging areas and summer habitat needs, and winter surveys monitor hibernating bat populations. A 2003 study indicated that little brown bats spend more time foraging over water, while Indiana bats spend more time in the drier lowland forests. Telemetry was also used in an effort to locate more Indiana bat nursery sites. Eleven female Indiana bats were radio-tagged in the spring as they exited the mine. None of the tagged bats remained in the park, and it appears that most of the Indiana bats from the mine are moving east for the summer months. A more extensive survey will take place in 2005.