"Natural Areas" are defined as "an area of land or water owned in fee simple or as a conservation easement by the Department, which has retained its natural character, although not necessarily completely undisturbed, or having rare or vanishing species of plant or animal life, or having similar features of interest, which are worthy of preservation for present and future residents of the State". (N.J.A.C. 7:5A-1.3). There are two Natural Area areas that can be found within the Delaware and Raritan Canal State Park, the Cook Natural Area and the Bull's Island Natural Area.

The Bull's Island Natural Area is located in Delaware Township, Hunterdon County. It is comprised of a lowland floodplain dominated by enormous tulip poplar, sycamore and silver maple. It is an excellent area for bird watching, especially during spring before all the trees leaf out. You can find a variety of birds including several species warblers, including the Prothonotary, Yellow-throated, and Cerulean. Just be careful to stay on the trail because stinging nettle grows in large patches beside the edge of the mile trail (along with american bamboo, jewelweed and wingstems). This area is also a provides a moist, shaded habitat for ostrich ferns, these ferns grow to 4 feet and are a commonly found in the Bull's Island Natural Area.

Grace Cook of South Brunswick generously donated the Cook Natural Area, located on Heathcote Brook Road in Kingston, to the State in 1970. Mrs. Cook stipulated that the property be "so managed and regulated by the State as to promote the enjoyment of natural things including trees, birds, wildlife and water, to educate the public as to the importance of ecology to all life including man's, and to nurture plants and animals for agricultural, horticultural, scientific and recreational purposes." The short trail (1/2-mile to 1 mile) will lead you through freshwater marsh and floodplain forested habitats and over a historic bridge crossing the Heathcote Brook. A large variety of plant species can be found here including members of the mint family, purple loosestrife, bulrushes and knotweeds. Tree species consist of River Birch, Pin Oak, Red and Silver Maple just to name a few.

Foot traffic only in both natural areas.