The Service's primary focus at Petit Manan is colonial seabird restoration and management. Refuge islands provide nesting habitat for common, Arctic, and endangered roseate terns, Atlantic puffins, razorbills, black guillemots, Leach's storm petrels, laughing gulls, and common eiders. Over the last 25 years, the Service and its conservation partners have worked to reverse the decline in these birds' populations. As a result, many species have returned to islands where they nested historically.

In addition to seabirds, wading birds and bald eagles nest on Refuge islands. The mainland divisions provide habitat for songbirds, shorebirds, and waterfowl, as well as opportunities for bird watching and hiking.

The Refuge's three mainland properties are located in Hancock and Washington counties. Upland areas are characterized by spruce-fir forests with some mixed hardwoods. The 2,166 acre Petit Manan Point Division, in Steuben, also includes jack pine stands, coastal raised heath peatlands, blueberry barrens, old hayfields, freshwater and salt water marshes, cedar swamps, granite shores, and cobble beaches. During the fall migration, 80-acre Cranberry Flowage is filled with over 4,000 ducks. Black ducks, green-winged teal, and mallards rest and feed there on wild rice before migrating south. The Gouldsboro Bay Division, in Gouldsboro, protects 600 acres, including a large tidal salt marsh and mud flat. The 628 acre Sawyer's Marsh Division lies at the head of a broad salt marsh in Milbridge, just north of Petit Manan Point.