
The Wallkill River is one of the few large rivers in the United States that flows north. From its headwaters in spring-fed Lake Mohawk, located in Sparta, New Jersey, the river flows north into New York State. It joins the Rondout Creek in Rosendale, New York and empties into the Hudson River in Kingston, New York. The Refuge is part of the Hudson River-New York Bight watershed.
The Wallkill River National Wildlife Refuge is currently participating in watershed planning of the Wallkill River.
The Refuge provides habitat for 73 types of vertebrate and invertebrate wildlife that are listed as endangered, threatened, special concern, or priority species.

Potential habitat exists in the Wallkill River for the Federally endangered dwarf wedgemussel (Alasmidonta heterodon). The New Jersey Division of Fish and Wildlife, Endangered and Nongame Species Program conducted surveys for this species in segments of the river running through the Refuge in 1999 (USFWS 2001) and 2001. These surveys did not detect dwarf wedgemussels or their shells. However, numerous stretches of suitable habitat were found consisting of sandy substrate or sand patches, little to no silt, and slow to moderate current. Additionally, the mussel's host fish, the tessellated darter (Etheostoma olmstedi), occurs in the river. Further, four freshwater mussel species that are often associated with dwarf wedgemussel occurrences were found.
There are 3 nature trails for wildlife observation, three fishing access sites on the Wallkill River and three canoe access sites. The refuge also provides hunting opportunities.
As of 2007, the refuge encompassed about 5,100 acres. Land acquisition is still proceeding. The refuge enjoys strong support from the community.