There are three North Carolina Wildlife Resources Commission boat ramps, suitable for small boats, near the refuge; one off of Mashoes Road provides access to East Lake, another off of Old Ferry Landing Road provides access to Alligator River, and a third at the end of Stumpy Point Road provides access to Stumpy Point Bay and Croatan Sound. There is also a boat launch at the end of Pamlico Road.
Operating any vehicle or boat that does not bear valid license plates or identification numbers and that is not properly lighted, certified, registered, or inspected according to State laws is prohibited. Leaving boats on the refuge overnight is prohibited.