The Refuge does not actively manage water levels in the lake. The primary purpose of the Refuge is to protect and conserve migratory birds and other wildlife through the protection of the wetlands. The best way to achieve that end is to allow the lake levels to rise and lower naturally. Specifically, flapgates facilitate the flow of water from the lake to Pamlico Sound when lake levels are higher than sound levels. When the lake falls below the levels of the sound, the gates close to prevent saltwater from entering the lake. Lake levels tend to be higher during the rainy season (winter) and lower during the dry season (summer). The lower lake levels in the summer spur the growth of emergent and submergent wetlant plants that are used by migrating and wintering waterfowl.
The Refuge also periodically dredges portions of the four canals connecting the lake to the sound. Maintaining the original depth of the canals improves their flushing capacity, which keeps the lake healthy by removing excess nutrients and sediments and allows the canals to move more water during storm events to prevent flooding. In addition, fish utilize the deeper water in the canals when the lake temperature rises.