Geologically, San Clemente Island is the upper part of a tilted and gently arched block of Earth's crust, composed primarily of volcanic rock. Its northeastern slope drops steeply into the Pacific, while the southwestern side descends more gradually. A major fault parallels the northeast boundary, part of the same system that has shaped the California coast. The island offers some of the finest examples of marine terraces anywhere, stair-stepped benches carved by ancient seas. Trench-like canyons cut through the landscape, fed by streams that create periodic waterfalls and pools of fresh water. Mount Thirst, the highest point, rises to 1,965 feet. The Mediterranean climate brings warm, dry summers and mild winters, with fog providing crucial moisture for the unique vegetation.

San Clemente Island harbors 15 plant species that exist only here. The San Clemente Island brodiaea, San Clemente Island triteleia, San Clemente Island woodland star, and San Clemente Island Indian paintbrush bloom in spring. The endangered San Clemente Island loggerhead shrike hunts from exposed perches, while the San Clemente Island fox prowls the scrublands. Feral goats once threatened everything, their population reaching 11,000 by 1972. The Fund for Animals blocked plans to shoot them, so the Navy removed the remaining goats with nets and helicopters, creating a recognized domestic breed in the process. Now bald eagles nest here again after decades of absence caused by DDT contamination. Peregrine falcons have returned as well. The coves teem with sea lions, spiny lobsters, and kelp forests that draw snorkelers to the abundant marine life.

Before the Navy arrived, San Clemente Island attracted a colorful cast of characters. Ranchers, fishermen, and smugglers used the island throughout the 19th and early 20th centuries. Whaling ships anchored in Pyramid Cove to process blue, fin, and humpback whales caught by steam-driven whale catchers. The steamship Lansing operated there between 1926 and 1930, the schooner California between 1933 and 1937. In 1935, the Norwegian factory ship Esperanza hunted blue whales in these waters. The Navy acquired the island in 1934 and transformed it into a training ground for the amphibious landing craft that would prove crucial to World War II. Today it hosts a $21 million simulated city for commando training and active sonar facilities.

The military mission carries real risks. On July 30, 2020, an amphibious assault vehicle carrying sixteen Marines and a sailor sank during a training exercise off the island's northwest coast. Eight Marines and one Navy sailor died. The AAV was found in nearly 400 feet of water. Less than a month later, on August 27, 2020, two soldiers were killed and three injured when their Black Hawk helicopter crashed on the island. These tragedies underscore the dangerous nature of the realistic training that San Clemente Island was designed to provide. Test rockets from the Polaris program launched from here between 1957 and 1960, and the SEALAB III underwater habitat project took place in these waters in 1969.

In 2008, earthworms arrived on San Clemente Island for the first time, hitchhiking in soil brought from the mainland for a road construction project. This might seem harmless, but the island had evolved without earthworms for millions of years. The worms are now altering soil structure and microbial communities, creating conditions that favor non-native plants over the endemic species that make San Clemente Island unique. Scientists worry that this seemingly minor introduction could threaten the biodiversity that exists nowhere else. It is a reminder that even on a remote, Navy-controlled island, human activity can have unintended consequences that ripple through fragile ecosystems.