View of one of the Refuge's managed wetlands

Since 1985, Back Bay National Wildlife Refuge has hosted a white-tailed deer hunt to keep the population of this native species in balance. The hunt is concurrent with one at False Cape State Park, south of the refuge. Hunters are selected by state lottery and assigned a one-day hunt in a specified hunting zone. Registration and a hunter safety orientation are held before transporting hunters to their selected zones. Hunters may use shotgun, 20-gauge or larger, loaded with buckshot or slugs. Crossbows, bow and arrow, and muzzleloader are not permitted. Selected hunters are encouraged to scout hunt zones before the hunt. When scouting, hunters must check in and out at the refuge visitor center and must wear a blaze orange hat and body covering to identify that they are engaged in scouting activities. No weapons are allowed during the scouting trips. When visiting to scout, parking is available at either the refuge or Little Island City Park. Parking fees apply; biking is recommended. Zone 5 is reserved for hunters with disabilities; hunters must provide their own transportation to the hunting area. October dates for the white-tailed deer hunt may vary. Please visit the refuge website for more information. Hunters are limited to two deer per day. Using state Deer Management Assistance Program tags, hunters will be allowed to take antlerless deer (does and fawns, buttons on males must be below the fur) without using big-game tags. If you take bucks with buttons or antlers above the fur, big-game tags will be required. In the past, feral hogs were permitted to be taken during the deer management hunt. Feral hogs are no longer found at the refuge and are not part of this deer management hunt. No deer hunt was conducted in 2017-2021. The refuge evaluates the deer population annually to determine the need for the hunt.

On years when a deer management hunt takes place, Back Bay Refuge works with adjacent False Cape State Park to offer select hunt dates in October. A total of 116 hunters are chosen through a state-run lottery system. Interested parties may apply for either the Refuge or False Cape State Park. Hunters may also hunt stand-by on the day of the hunt. Scouting is encouraged during daylight hours the week prior to the hunt dates.

Waterfowl hunting is prohibited in waters within the Presidential Proclamation Boundary and on all refuge lands.