Cherry Valley National Wildlife Refuge was established in part to protect the federally threatened bog turtle, which can be found in wetlands throughout the valley. Due to their listed status, refuge public use areas are located away from sensitive bog turtle habitats.
 

The Kittatinny Ridge (which flanks the south side of the valley) has been designated an Important Bird Area by the Pennsylvania Audubon Society, and is a well-known migration flyway that concentrates up to 20,000 migrating raptors and more than 140 bird species every fall.
 

The most well-known mammal species in Cherry Valley are game animals, including black bear and white-tailed deer. Squirrel, raccoon, woodchuck, skunk, and opossum are found in the more developed areas of the watershed. Common furbearers include mink, muskrat, beaver and otter.
 

The valley’s ridges and hills are cloaked in mixed hardwood and conifer forest, while chestnut oak, gray birch, quaking aspen, white pine, and pitch pine populate flat ridge tops once cleared for pasture and logging. Some juniper and Virginia pine can be found on recently abandoned farmland. Oaks, red maple, black cherry, hemlock and tulip poplar dominate in other areas. These upland forests are the most common habitat type and total nearly 18,800 acres, nearly 60 percent, of the valley.
 

In most areas of the valley, riparian vegetation is well‐established and stable, providing a thick canopy important to fish. In addition to streams and creeks, a variety of forested and open wetlands are found in the valley bottom and total nearly 1,750 acres. These wetlands host a variety of wildlife including waterfowl, wading birds, river otter, beaver, and several dozen species of reptiles and amphibians. Vernal pools are also scattered across the valley, supporting a number of salamander, frog, turtle, and snake species.