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Aleuts hunters visited the Islands to hunt otters in the early 1800s. The Aleuts purportedly clashed with the native Chumash, killing many over trading disputes. Aleut interactions with the natives were also detailed in O'Dell's book.

Several of the islands were used by whalers in the 1930s to hunt for fin whales.

San Nicolas Island has been used since 1957 as a launch pad for research rockets. San Nicolas was considered out of eight possible locations as the site of the Trinity bomb test, or the first nuclear bomb detonation.

San Clemente Island was used to train the Navy's first amphibious force to prepare for Pacific combat against the Japanese in World War II.

The Islands still house US Navy SEALs training facilities and continues to use the Naval Auxiliary Landing Field located on San Clemente Island.

Visitation
The Channel Islands National Park's mainland visitor center received 342,000 visitors in 2014 The Channel Islands itself attracts around 70,000 tourists a year, most during the summer. Visitors can travel to the islands via public boat or airplane transportation. Camping grounds are available on Anacapa, Santa Rosa, Santa Cruz, San Miguel, and Santa Barbara Islands in the Channel Islands National Park. Attractions include whale watching, hikes, snorkeling, kayaking and camping.

Conservation
Conservation efforts are being made to maintain the endemic species' numbers. Feral livestock, including pigs, goats, and sheep, pose a threat to many of the endemic species, including the San Clemente Loggerhead Shrike and Channel Islands Spotted Skunk. The National Parks Services eradicated the feral pigs on Santa Rosa and Santa Cruz islands during the 1990s in order to protect the islands' wildlife. Introduced pathogens have devastated island species due to isolation from the mainland. In 1998, an outbreak of canine distemper swept through Santa Catalina Islands severely reducing the island skunk and fox populations. Rabies and distemper vaccination programs were initiated to protect the island's wildlife. Canine distemper is thought to have been brought to the islands on a stowaway raccoon or a domestic dog. In 2011 on Santa Rosa Island, introduced deer and elk were exterminated.

Flora
Flora on the Channel Islands include a unique subspecies of Pine, Oak, and the Island Tree mallow. Santa Rosa Island holds two groves of the Torrey Pine subspecies Pinus torreyana var. insularis which is endemic to the island. Torrey Pines are the United States' rarest pine species. . The Islands also house many rare and endangered species of plants, including the Island Barberry, the Island rushrose, and the Santa Cruz Island lace pod. Giant kelp forests surround the islands. These forests act as a source of nutrition and protection for other animals.

Invasive species, such as the Australian blue gum tree, olive tree, sweet fennel and Harding grass threaten native species through competition for light, nutrients, and water. The Australian blue gum, for example, releases toxins in its leaf litter which prevents other species of plants from growing in the soil surrounding it. The blue gum, as well as other species including the Harding grass, are much more flammable and better adapted to wildfires than native species.

Fauna
The Channel Islands and the waters surrounding hold many endemic species of animals, including fauna such as the Channel Islands Spotted Skunk, Island Scrub Jay, Ashy Storm-petrel, Santa Cruz sheep, San Clemente loggerhead shrike, San Clemente sage sparrow. Many species of large marine mammals, including pacific grey whales, blue whales, and California sea lions breed or feed close to the Channel Islands. Seabirds, including the western gulls, bald eagles, pigeon guillemonts, and Scripps's murrelets use the islands as well for shelter and breeding grounds. The endemic Island Fox is California's smallest natural canine and has rebounded from its near extinction in the late 1990s. Several endemic reptile species including the Island fence lizard, Island Night Lizard, and Channel Islands Slender Salamander live on the islands.

In the 1950s, bald eagles and peregrine falcons on the Channel Islands became locally extinct after widespread use of pesticides such as DDT. The birds ingest contaminated fish and fish eating birds which weakens their eggs. Golden eagles, which are natural competitors of other birds of prey, do not primarily feed on these animals and were able to colonize the islands in the early 1990s. In the early 2000s, golden eagles were live trapped and relocated. In 2002 and 2006 breeding pairs of bald eagles were reintroduced to the northern islands. Later in 2006, the introduced adult eagles hatched chicks on the islands for the first time in 60 years. The Channel Islands National Park established a bald eagle webcam on their website.