A natural area is an area of unique scenic, historical, geological or ecological value, maintained in a relatively undisturbed manner where natural succession will be allowed to occur.

Six natural areas have been designated on the Delaware State Forest. Bruce Lake Natural Area covers 2,845 acres including two lakes, Bruce Lake and Egypt Meadow Lake. Bruce Lake was formed during glaciation and is completely spring fed. Virgin stands of pine and hemlock were cut in the late 1800s leaving the area vulnerable to fires that destroyed the rich humus soil layer. Egypt Meadow Lake was constructed by the Civilian Conservation Corps in 1935.

During the Civil War, the Stillwater Natural Area provided a sanctuary for Union Army deserters and young men evading conscription. Shacks were built on the islands of the swamp or in the dense growth. This 1,931-acre tract contains a mix of conifers and hardwoods. About one mile of the Little Bushkill Steam offers "stillwaters" for canoeing.

Scrub oak, gray birch, aspen, and mixed oaks dominate the landscape of Pennel Run Natural Area. This elevated area comprises of 936 acres. A portion of the Utts Swamp is located within this natural area. A high mountain swamp surrounded by mixed oaks is located within the 535-acre Buckhorn Natural Area. Reptiles and amphibians are protected by special regulations within Pennel Run and Buckhorn Natural Areas.

Pine Lake Natural Area is a 67-acre site. Included is a 10-acre glacial bog that exhibits plant zones ranging from open water to tree cover. Various flora and fauna inhabit this tract.

A boreal conifer swamp is located within the Little Mud Pond Swamp Natural Area. Various emergent plants grow within the glacial bog. Species normally found at more northern latitudes can be found on this 182-acre tract.