In a broader sense, Barnegat Bay is sometimes considered to stretch to the south end of Long Beach Island and to include Little Egg Harbor.

The Barnegat Division of Edwin B. Forsythe National Wildlife Refuge comprises wetlands along the inner southern part of the bay.

The bay was originally named in 1614 "Barendegat," or "Inlet of the Breakers," by Dutch explorers of the coastline, referring to the waterway's turbulent channel.

[3] The song "My Eyes Adored You", by New Jersey native Frankie Valli, contains a reference to "walking home every day over Barnegat Bridge and Bay".

[4][5] In the 2000s and 2010s, scientists and residents have drawn attention to fish kills, algal blooms, low dissolved oxygen levels, loss of habitat, diminishing clam populations, and the rise in stinging Chrysaora quinquecirrha (sea nettle jellyfish) populations in the bay, mainly due to high levels of nitrogen from fertilizer runoff.

[6][7][8] The U.S. Environmental Protection Agency monitors the health of the bay by testing at four locations as frequently as once a week in the summer months, when surface water can reach 82 °F (28 °C).

[9] Community members have also expressed concern over the impact of stored radioactive material and thermal pollution at the Oyster Creek Nuclear Generating Station in Lacey Township.

[11] A 2008 baseline sediment pollution study of 15 locations within Barnegat Bay - Little Egg Harbor area including sites at Mill Creek, Cedar Run, Parker Run measured total petroleum hydrocarbons, mercury, polyaromatic hydrocarbons (PAH) and polychlorinated biphenyls (PCB).