Great Bay is located in southern New Jersey's Atlantic Coastal Plain in Ocean and Atlantic Counties, about ten miles (13 km) north of Atlantic City and 87 mi (140 km) south of New York City. The Mullica River flows into the bay, and together they form the Mullica River - Great Bay estuary habitat. The bay is connected to the Atlantic Ocean via the Little Egg Inlet. Great Bay is considered one of the least-disturbed marine wetlands habitats in the northeastern United States.
Great Bay averages about 1.5 meters (5 ft) in depth, and extensive areas of the estuarine substratum are covered with benthic algae and some vascular plants (seagrasses). Eelgrass (Zostera marina) beds are an important component of the submerged aquatic vegetation (SAV) community in Great Bay, generally where depths are 1 meter (3.2 ft) or less but, due to the slightly greater depth in Great Bay, these are not as ubiquitous as they are in the Barnegat/Manahawkin/Little Egg system to the north. Extensive areas (13.58 km² [3,355 acres]) of intertidal sandflats and mudflats occur in the bay, a result of the sediment load from the Mullica River and the movement of sand in through Little Egg Inlet.
Finfish make up an important component of the bay's ecosystem. The bay provides an important nursery area for bluefish, weakfish, menhaden, and spot (Leiostomas xanthurus), as well as spawning habitat for winter spawners such as sandlance (Ammodytes americanus) and winter flounder and summer spawners like bay anchovy (Anchoa mitchilli), silversides (Menidia spp.), gobies (Gobiosoma spp.), wrasses (Labridae spp.), and northern pipefish (Syngnathus fuscus).