Geologically, the island is described as being "the upper part of a tilted and gently arched northwestward-trending block of the earth's crust that has a straight, steep northeastern slope and a more irregular and much gentler southwestern slope" that is composed primarily of volcanic rock, with the northeast boundary of the island having a large fault that parallels most of the major faults on the California mainland.

San Clemente Island has some of the best examples of marine terraces and has trench-like canyons, streams, periodic waterfalls, and pools of fresh water.

[7] This region experiences warm and dry summers and moderate mild falls and winters with no average monthly temperature above 21 °C (69.5 °F).

[8] The San Clemente Island loggerhead shrike is an endangered species that the Navy is taking steps to protect.

The coves around the island are visited by snorkelers attracted by the abundant marine life, including sea lions, spiny lobsters, hydrocoral and kelp forests.

In this earthworm-free region, the worms alter the soil and microbial communities, which allows non-native plants to change the island’s unique ecosystem and threaten biodiversity that exists there.

[18] Archaeologists have found traces of human occupation on San Clemente Island dating back 10,000 years.

Later, inhabitants left trade materials from the northern islands and the mainland, including Coso obsidian from the California desert.

It has not been established what tribe the recent inhabitants belonged to, although the Tongva, who are well attested from Santa Catalina Island, are the most likely candidates.

[25] In 1935, the Norwegian factory ship Esperanza caught blue whales as far north as San Clemente Island.

[27] Seven marines and one Navy sailor were presumed to have died when their amphibious assault vehicle (AAV) sank during a training exercise off the island's northwest coast on July 30, 2020.

[31] On 27 August 2020, two soldiers were killed and three were injured when their Black Hawk helicopter crashed on San Clemente Island.