Spanish explorers and missionaries reached the area in the 1700s and established Mission San Juan Capistrano, whose lands included part of the Aliso Creek watershed.

After California became part of the United States, the ranchos were gradually partitioned and sold off to farmers and settlers; starting in the 1950s, real estate companies acquired most of the land for development.

Past Muirlands Boulevard the creek flows in a concrete channel, making a sharp turn to the southeast before veering back south towards Interstate 5.

Below this point the valley widens at the northernmost tip of Aliso and Wood Canyons Wilderness Park, the beginning of a greenbelt that stretches from here nearly to the Pacific Ocean.

[34] Before urbanization of the watershed, Aliso Creek and some of its tributaries supported a significant riparian zone dominated by native hardwoods such as coast live oak, sycamore, alder, cottonwood and arroyo willow.

The U.S. Army Corps of Engineers describes the corridor as "meager at best with several places where Aliso Creek is very narrow, concrete, or incorporates golf courses parks and school grounds.

Fish and Wildlife Service designated the Aliso Creek estuary and several other coastal Southern California streams as critical habitat for the tidewater goby.

[49] D. Earle (1992) further stated that "There is some evidence... that Gabrielino (Tongva) territory may have extended only as far south as the Tustin Plain" (a location about 10 miles (16 km) north of Aliso Creek).

[51] This contradicts the generally accepted theory originated by Alfred L. Kroeber (1925) who stated that "Juaneño (Acjachemen) place names do not extend north of Aliso Creek".

[51] On July 24, 1769, the Spanish Portolà expedition led by Gaspar de Portolá, traveling north from San Diego, reached a stream which Fray Joan Crespí described as "Alisos Creek", which was actually the Arroyo Trabuco.

Crespí wrote in his diary, "So we went on over very open country, with hills and broad mesas, ascending and descending through three or four little valleys of good soil well grown with alders."

Don Juan became known as "El Rico" for his wealth and hospitality; he made a fortune driving beef cattle up to Northern California after the gold rush started in 1848.

Don José also had a racetrack and rodeo grounds near Aliso Creek, near the present day intersection of El Toro Road and Muirlands Blvd.

There is no trace today of the original Serrano residence, although its precise location has been identified in Sycamore Park in Mission Viejo, on the east bank of Aliso Creek north of I-5.

It served as a Girl Scout camp for several years before the Laguna Beach Country Club, the precursor of the present day hotel and golf course, was built in 1950.

[63] After the severe drought of 1863–64, in which thousands of cattle died, Don José Serrano was forced to sell the Rancho Cañada de los Alisos to J.S.

By 1932, citrus and other fruit trees were the main crops in El Toro, irrigated by wells sunk into the shallow groundwater basins along Aliso creek.

[15] For similar reasons, Don Juan Avila sold the Rancho Niguel in 1865 to John Forster, and the property was eventually purchased by Lewis Moulton and Jean Pierre Daguerre in 1895.

Daguerre was one of many Basque immigrants who arrived in this part of Orange County starting in the 1870s, introducing sheep ranching and crops of bean and barley to the area.

[77][78] The creek contains elevated levels of E. coli, phosphorus, nitrogen and selenium, which comes mainly from heavy application of fertilizer and manure, and other organic pollutants in urban runoff.

[80] Runoff of chlorine, oils and heavy metals,[79] mainly caused by irrigation and car washing, have killed off most fish and shrimp species in the creek, with the exception of carp.

Officials from the Orange County Environmental Health Department say that skin rashes, infections, "pink eye" and other assorted ailments are not uncommon to those who use Aliso Beach and, unwittingly, come in contact with the creek and its invisible bacteria...".

The obstruction of natural sediment sources and increased water flow due to urban runoff has caused significant downcutting in the river bed.

[41] The project would remove the existing drop structures and barriers along this section of the creek and construct 47 low rock riffles to maintain a constant gradient.

Water flows into a series of pools where it is filtered by vegetation and bacteria are killed by prolonged exposure to sunlight, before entering 25 acres (10 ha) of restored riparian habitat along Aliso Creek.

[93] In October 2017 the Laguna Ocean Foundation presented a concept restoration plan for the Aliso Creek estuary, which was endorsed by Orange County Supervisor Lisa Bartlett and Senator Patricia Bates (R-Laguna Niguel).

[94] The project would remove a parking lot and artificial turf on the north side of Highway 1 in order to restore the estuary to its original 14-acre (5.7 ha) size.

This would lower the frequency with which water breaches the sandbar separating the estuary from the Pacific Ocean, enhancing habitat stability for species such as the tidewater goby and western pond turtle.

[103] Laguna Niguel Lake is regularly stocked with catfish, bass, bluegill, and trout during the winter months, and offers both shoreline fishing and boat rentals.

In March 2015 Mark Christy, the new owner of the resort, agreed to commit $250,000 towards designing a trail through the property as part of the new "Ranch at Laguna Beach" development, though no date has been set for its completion.