The 1,068-acre Carlton Pond WPA includes most of Carlton Pond, the surrounding freshwater wetlands, and several small areas of forested lowlands and uplands. More than 84 percent of the site is open water or shallow freshwater marsh. The remaining 16 percent is forested, dominated by aspen, red and sugar maple, box elder, paper birch and eastern white pine. The Service has access to the dam via a right-of-way through a private residence off Route 220 in Troy. There is no established public access to Carlton Pond. Boaters and anglers put in at one of the inlets along Bog Road.
At capacity the pond itself consists of approximately 285 acres of open water containing 1,198 acre-feet of water. Emergent plants such as pickerel weed, pond lily, and water lilies are abundant. The original dam at Carlton Pond was a rock structure built in 1850 to provide waterpower for a sawmill operation. In 1972, the dam was reconstructed with a water control structure to maintain the integrity and to ensure continued maintenance of the open water and wetland areas created by the original dam. The water control structure was rehabilitated in 1996, with assistance from Ducks Unlimited.
Carlton Pond WPA has historically provided good nesting habitat for waterfowl and other birds. To date, over 33 bird species have been observed using refuge lands and waters. Many bird species that use Carlton Pond have been listed by the Partners-in-Flight organization as species that are declining.
Surrounding the open water is a freshwater wetland with plants typical of a grassy marsh and including leather-leaf, buttonbush, cranberry, sweet gale and rhodora. Slender Blue Flag, a species listed as Threatened by the State of Maine, has been sighted at Carlton Pond.