In April 1942, the City of New York started placing hydraulic fill over the marshy tidelands of the area.

[3] The extent of the refuge is mostly open water, but includes upland shoreline and islands with salt marsh, dunes, brackish ponds, woodland and fields.

[4] Originally created and managed by New York City as a wildlife refuge, the term was retained by Gateway when the site was transferred in 1972.

The primary diet of the diamondback terrapins include fish, snails, worms, clams, crabs and marsh plants, many of which are abundant in these particular marshlands.

The recently increased raccoon population, however, has developed a taste for diamondback terrapin eggs, and many nests are often destroyed only 24 hours after being laid.

[17] The refuge attracted species such as black skimmers and snowy egrets, which had not been seen in the New York City area in several decades.

[22] As a result of climate change, the Jamaica Bay area faces effects such as salt marsh erosion, rising sea levels, and flooding.

[23] In 2012, Mayor Michael R. Bloomberg and Secretary of the Interior Ken Salazar authorized the creation of the Jamaica Bay-Rockaway Parks Conservancy, Inc.

[17] A $400 million restoration project was begun in 2018 to combat erosion and pollution, remove maritime debris, and clean up storm damage remaining from Hurricane Sandy.