The three main islets, East, Middle and West Anacapa, have precipitous cliffs, dropping off steeply into the sea.

[8][1] These eruptions are believed to have been caused by thinning of ocean crust as the block containing the northern Channel Islands and Santa Monica Mountains was rotated clockwise by the transverse motion of the Pacific and North American plates.

[1] Erosion has heavily weathered the lava formations of Anacapa, and wave action caused the island to split into three islets in recent prehistoric times.

As recently as the end of the last ice age (about 10,000 years ago), sea levels as much as 400 ft (122 m) lower than today meant that the four northern Channel Islands were part of a single large island (dubbed "Santa Rosae") that lay about 5 miles (4 nmi; 8 km) off the California coast.

Great white sharks, feeding on pinnipeds, are found in the waters of the Channel Islands, including Anacapa.

The only native land mammal on the island is a unique subspecies of deer mouse (Peromyscus maniculatus anacapae) which occurs on all three islets, but nowhere else.

The prolific seeds provided abundant food for the endemic Anacapa deer mouse, and for many small birds.

The island's stands of giant coreopsis, as well as all the other plants of its coastal bluff community, were devastated by sheep grazing in the late 1800s and early 1900s, rabbit browsing in 1910-1950s, and by large-scale destruction of native vegetation associated with facility and road development by the United States Coast Guard during construction and manning of the Anacapa Light Station.

Introduced mammals on Anacapa Island included domestic cats, sheep, rabbits, and black rats.

[15] The rats were certainly introduced sometime prior to 1939 (when they were noted by National Park Service researchers Sumner and Bond), probably in supplies brought onto the island for sheep ranching or building the lighthouse.

[14] European rabbits were introduced to East Island either as an emergency food supply for lighthouse personnel during World War II or as pets.

[21] Many writers reported that in the absence of springs on Anacapa sheep would lick the moisture that accumulated on each other's fleeces from the coastal fog.

[22] The native flora was affected by the forage grasses that farmers introduced to feed their flocks, and by soil-compaction caused by the sheep's hooves.

[26] Approximately 300 deer mice were captured prior to the application of rodenticide and reintroduced after poison levels had dropped, which was about three months.

[33] On the night of December 2, 1853, the sidewheel steamer SS Winfield Scott, running at full speed, crashed into the rocks off Middle Anacapa and sank.

Ira Eaton acquired the lease in 1917 and held it until 1927, and used the island for his bootleg alcohol operation during Prohibition in the United States.

[33]: 170–174 On a visit around 1910, Charles Frederick Holder noted "kitchen-middens, and deposits of ancient shells, and the tell-tale black earth" of hearths.

The U.S. Coast Guard still owns the property, but the National Park Service moved into the residences in 1970, while sharing the wharf and hoist facilities.

[33]: 177–179 On January 31, 2000, Alaska Airlines Flight 261 crashed near the island following a catastrophic loss of pitch control caused by jackscrew, killing all 88 people aboard.

The official 2000 census population was three permanent residents, all at the ranger station in the eastern part of East Island.