It consists of a main building with exhibits on local natural history and archeology, including an outdoor butterfly house and 400 acres (160 ha) of museum- and town-owned conservation land with walking trails.

The combined land covers a wide range of habitats, including pitch pine woodlands, salt marshes, a barrier beach, beech forests, and a small river, Stony Brook, which functions as a herring run during the spring.

[6][7] The museum houses exhibits on topics related to local natural history and archeology, including a small aquarium featuring over eighty different species of local freshwater and saltwater marine life, a butterfly house, several beehives, a collection of taxidermied birds, and a collection of wooden birds carved by Eldridge Arnold.

[3] The museum's Marshview Room provides a view over conservation lands with binoculars for birdwatching and a monitor displaying a livestream of the osprey nest in the marsh.

In addition to its exhibits, the Cape Cod Museum of Natural History engages in educational outreach such as summer programs for children, classes and lectures, and live-streaming webcams showing a view of nesting birds.