The park includes trails for hiking, mountain biking, and horseback riding; a greenbelt and bikeway along Aliso Creek; and various geological features such as caves, springs, and exposed marine fossil beds.

[4] The park was originally inhabited by the Acjachemen and Tongva Native Americans who used Aliso Creek as the boundary between their respective territories to the south and north.

Because Aliso Canyon was one of the few places in what is now south Orange County with perennial streams and springs – as well as providing easy access from inland areas to the Pacific Ocean – it was a major wintering spot for native peoples.

Spanish ships were also known to anchor in the bay at the mouth of Aliso Canyon and sailors "harvested large timbers from the river area".

[6] In the following decades the Spanish colonized California they established missions to convert the Native Americans to Christianity with varying degrees of success.

The Aliso Canyon was the proposed location of a "much publicized national fitness center headed by former Los Angeles Rams coach George Allen.

[11] The canyon was spared from development when about 40 land parcels were acquired by the county for use as a park, the largest in 1979 when the Mission Viejo Company donated 3,400 acres (1,400 ha).

[20] Many of the names for smaller trails in the park are from the Acjachemen language, including Aswut ("golden eagle"), Toovet ("brush rabbit"), Alwut ("crow") and Hunwut ("black bear").

Sediment deposited by Aliso Creek slowly filled the canyon to depths of 13 to 36 feet (4.0 to 11.0 m) and created the flat valley floor seen today.

[23] The creek remains as an underfit stream whose present size, in today's semiarid climate, appears too small to have cut the canyon through which it flows.

The San Joaquin Hills consist of marine sedimentary rock that originally lay at the bottom of the Pacific Ocean before being uplifted above sea level.

[24] Limestone outcrops in the northeast section of the park, part of the Pecten Reef, have yielded thousands of fossils including Miocene dolphin and whales,[25] preserved invertebrates, plankton, bryozoa, and red, blue and brown algae.

[26] Much of the scientific understanding for evolution, paleoenvironments and paleoclimates during the Miocene period in Orange County is based on the specimens collected from the Pecten Reef.

Dam construction, upstream channelization, pollution, invasive plant species such as giant reed, as well as severe erosion problems that have in some places undermined the Aliso Creek Trail,[30] have essentially eliminated steelhead with only occasional anecdotal sightings.

[27] Among the most long-running problems afflicting Aliso and Wood Canyons is the presence of invasive species, many introduced by former ranching activities, and later, exotic ornamental plants imported for gardens.

Plants such as giant reed (Arundo donax) and pampas grass crowd out native vegetation and provide less nutritional value to animals that frequent the park.

There are also numerous invasive animal species, including the Brown-headed cowbird, a brood parasite which lays its eggs in native birds' nests.

Since then, the population of south Orange County has grown faster than projected, increasing the volume of wastewater entering Aliso Creek and causing erosion problems inside the park.

[11] In the 1990s Orange County and the Mission Viejo Company constructed a dam on Aliso Creek inside the park, which was intended to control erosion and help restore riparian habitat.

A 2008 proposal by the U.S. Army Corps of Engineers, would have "locked" the creek in place by building 20 drop structures and underground concrete walls to counter channel migration.

In 2009 a study submitted to the City of Laguna Beach suggested that the creek should be allowed to reach natural equilibrium with its surroundings, as additional human interference would likely lead to further unexpected damages.