Anacapa Island is predominantly volcanic in origin, composed mainly of highly weathered Miocene volcanic rock that has been eroded by wind and waves. It was probably uplifted not by volcanic activity, but by faulting. Many submarine lava flows can be seen on the island. In a few locations, sedimentary rocks can be found, including the blue-green San Onofre breccia on the south shore of West Anacapa near Cat Rock. Fissures forming sea caves and blow holes are common. Visually, Anacapa Island, along with the three other Northern Channel Islands represents a seaward extension of the Santa Monica mountains.

East Anacapa is the smallest of the three islets, rising from the sea as a seemingly inaccessible mesa. The slightly terraced top of approximately 100 acres lies about 200 feet above sea level. Facilities on East Anacapa include the fog signal. lighthouse, Park Service buildings, and campground.

Middle Anacapa Island is the second largest of the three islets. It is a little over three miles long, but seldom over 1/8 mile wide. Several small pocket beaches along the south side are only accessible by boat. East Fish Camp, the largest landing on the south side, was once the home of several fisherman. Landing is possible on the north side near the middle of Middle Anacapa  visitation is not permitted without permission from the Park Service.

West Anacapa Island is the largest, the highest, and the most topographically diverse of the three islets. Visitation is strictly limited to Frenchy's Cove and tide pool areas due to pelican and sea bird nesting activity.