The Wertheim National Wildlife Refuge on the south shore of Long Island is one of the last undeveloped estuary systems remaining on Long Island. Approximately half of the refuge consists of aquatic habitats including bay with marine seagrass beds, intertidal saltmarsh, high saltmarsh, freshwater marsh, shrub swamp, and red maple swamp. The refuge's saltmarshes, combined with the adjacent New York State-owned saltmarsh, form the largest continuous saltmarsh on Long Island.

The remaining half of the refuge is upland featuring the rare Pine Barren habitats of pitch pine, oak-pine, mixed oak, pioneer hardwood, upland shrub, and grasslands.

The refuge's wildlife populations are quite diverse. About 300 species of birds have been documented at Wertheim. The refuge winters up to 5,000 waterfowl, the majority being black ducks - a species in nationwide decline. The coastal location also makes this refuge an excellent migration corridor for shorebirds, raptors and songbirds.

The main purpose for establishing the refuge was to protect the Carmans River Estuary for migratory birds. The River is a NY State-designated Wild and Scenic river and one of the Island's largest. The refuge supports eight Federal and/or New York State protected species.