The site hosts breeding diamondback terrapin, seabeach amaranth, seabeach knotweed, Schweinitz's flatsedge, needlepod rush, and slender flatsedge. This is a critical saltwater wetland habitats supporting a renowned abundance and diversity of shorebirds, waterfowl, gulls, terns, and other species. The area is an important waterfowl wintering area as well with healthy numbers of scaup and Brant. Vandalia Dunes, a 230-acre site on the shore of the bay has been slated for 2,385 unit housing project with an adjoining shopping center, retail and office space, public schools, etc. A 302-acre site along the Atlantic Ocean beaches of the Rockaway Peninsula which hosts breeding Piping Plovers is also being considered for development.
Pollution is an ongoing problem, though great strides have been made in recent decades.
Sewage, storm drain outflow, and contaminated sediments are ongoing issues. Swimming and shellfish fishing are prohibited, and health advisories warn against fish consumption. The portions of the complex owned and managed by the National Park Service as part of the Gateway National Recreation Area are under competing pressures for various public recreational uses including biking, surf-fishing, sunbathing and swimming, musical concerts, and educational programs. These uses may sometimes conflict with needs of birds and other wildlife and should be considered carefully. Estimated numbers of individuals are included when available.