The canyon is a water gap across the San Joaquin Hills carved out by Aliso Creek, possibly as recently as the last ice age.

Located in a semi-arid climate, it supports a variety of plant communities – mainly chaparral and coastal sage scrub – and native animals, some endangered.

The fertile alluvial soil and grasslands of Aliso Canyon was used for orchards and grazing from Spanish conquest of the region until the early 20th century.

About 800 feet (240 m) deep on average and 1.5 miles (2.4 km) wide at its widest extent, it is one of the largest gaps through the San Joaquin Hills.

[2] The new rainy climate of Southern California received around 80 inches (2,000 mm) of rain each year, which caused the rivers and streams to become powerful and with enormous erosive force.

Near the end of the Wisconsinian, the canyon was already a 1,100-foot (340 m)-deep gorge with a narrow, powerful watercourse at the bottom; the valley floor was likely around 300 feet (91 m) wide.

Upstream development which has resulted in increased runoff with little sediment content has caused the creek to incise a 20-foot (6.1 m)-deep, 50-to-100-foot (15 to 30 m)-wide channel through the entire length of the valley.

The creek now is continuing to incise through the soft alluvial soil and a community of exotic giant reed has established itself throughout the length of the valley.

One is the paved Aliso Creek trail and one is an unpaved private road that leads to a wastewater treatment plant near the mouth of the canyon, owned by the South Orange Water Conservation Agency (SOCWA).

[5] The Aliso Canyon has four major vegetation zones; these are riparian, chaparral, coastal sage scrub and grassland.

It has been proven by a local NGO, CLEAN WATER NOW, that historically the Endangered Species Act listed Southern steelhead trout in 1997 as having spawned and resided in the creek.

The northern drainage divide of the gorge marked the boundary in this area, and the Acjachemen settled in small villages all along the valley floor.

In 1871, pioneer Eugene Salter settled at the canyon mouth, but one year after, sold it to the Thurstons, who cultivated the present-day golf course area as an orchard.

A later project to restore a riparian zone in the canyon, the Aliso Creek Wildlife Habitat Enhancement Project (ACWHEP) involved damming the creek and constructing pipelines from the impoundment to irrigate artificial creekside terraces of native plants, as well as prevent further erosion of the canyon floor by urban runoff.

Due to a flaw in the design, the dam actually caused further erosion, and the irrigation pipes are now broken and the terraces lie fallow.

[4] The Pecten Reef in the northeast section of the canyon area is an above-ground exposure of the Monterey Formation, which dates back to the Miocene period.

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.