Great Bay averages about 1.5 meters (4.9 feet) in depth, and extensive areas of the estuarine substratum are covered with benthic algae and some vascular plants (seagrasses).

Extensive areas (13.58 km2 (3,360 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.

The top ranked fish by their relative abundance were: bay anchovy (Anchoa mitchilli), Atlantic silverside (Menidia menidia), silver perch (Bairdiella chrysoura), alewife (Alosa pseudoharengus), striped killifish (Fundulus majalis), sea herring (Clupea harengus), white perch (Morone americana), northern puffer (Sphoeroides maculatus), oyster toadfish (Opsanus tau), and striped anchovy (Anchoa hepsetus).

Also included in the habitat complex are several small palustrine (nontidal) wetlands immediately adjacent to the estuary that contain exemplary rare natural communities and plant occurrences.

The coastal salt, brackish, and freshwater marshes in the Mullica River - Great Bay estuary are extremely important to waterfowl, raptors, wading birds, and shorebirds.