The barrier island and associated tidal marshes, creeks, and bays provide a diverse array of habitats for many species of birds throughout the year. American Oystercatchers and Willets are abundant and nest throughout the site, but no formal surveys have been conducted. In years past, terns and skimmers, nested on open, sandy areas. A great variety of shorebirds, wading birds and marshbirds are abundant during migration and winter months.

A jetty built to maintain a navigable channel in Masonboro Inlet is one of the few places in North Carolina with wintering Purple Sandpipers and often a Great Cormorant or two. Last year, a few Harlequin Ducks, a species that does not usually come this far south, excited local birders by wintering at the inlet. At the same time, the jetty causes accelerated erosion on the beachfront, which must receive dredged sand periodically to replace sand lost to erosion.

Disturbance to nesting birds is a critical conservation concern on the island. The island has heavy recreational use during the warmer months, especially on the northern and southern ends. This use has displaced nesting birds. In recent years, recreational use and unleashed pets appear to be increasing in the more remote areas of the island. This presents a significant problem for beach-nesting birds that have already abandoned the more heavily used areas of the island. Abundant raccoons and red foxes threaten nesting shorebirds and waterbirds. Most nesting shorebirds and waterbirds are not successful at fledging chicks.