[17] The eastern wall of the canyon consists of a slope that leads to Spooner's Mesa,[18] which was named after a couple who had a homestead atop it.

[19] Numerous sensitive[Notes 1] and endangered plant species including the southern willow, mule fat, maritime succulent scrub varieties; and endangered animals including least Bell's vireo, Belding's savannah sparrow, and California gnatcatcher are found within Goat Canyon.

[22][23] In the area surrounding the canyon, evidence of human activity relating to the San Dieguito and La Jollan prehistoric cultures has been found.

[25] In 1769, the Portolá expedition's overland group, with which Junípero Serra was traveling, traversed Goat Canyon on their way to San Diego Bay.

[15][26][27] In 1775, members of the Kumeyaay people living in the Tijuana River Valley, of which Goat Canyon forms the southwestern portion, attacked Mission San Diego de Alcalá, which Serra had helped found several years previously.

[30] Sometime after the end of the Mexican–American War in 1848 the land between Imperial Beach and Monument Mesa was owned by Elisha Babcock, who went on to develop Coronado.

[31] The land was passed to James Crafton, one of the owners of the Agua Caliente Casino and Hotel, around the time of the Great Depression.

[39] United States military activity near Goat Canyon began to the west with the surveying of a border marker.

[40][44][45] In 1943, on the south side of the base near the canyon, 35 buildings, including a trap house, were built close to Monument Road to support military operations at the airfield.

[44] Other users of the area were the California National Guard—which had launched pilot-less drones in the decade prior—and the Imperial Beach Police Department, which had a shooting range on the land.

[5] The construction of the highway and a concrete channel in the canyon on the Mexican side led to people moving into Cañón de los Laureles in an unplanned manner.

[60] By 1998, areas of low-income housing that were prone to damage during flash floods caused by seasonal rains had been built in the canyon.

[8][61] In 2001, a pipeline intended to send sewage from the canyon to the International Boundary Wastewater Treatment Plant was installed.

[62] A sediment basin was constructed at the mouth of the canyon in 2005 because significant amounts of material originating from south of the border were deposited in the Tijuana River Estuary, leading to loss of habitat.

[67] Even with the pipeline and later upgrades to the International Boundary Wastewater Treatment Plant, sewage still flows into Goat Canyon.

[70] By 2014, environmentalists were able to create a recognized watershed council; this gave the area political representation with the aim of increasing the infrastructure within the Mexican portion of the canyon.