[3] The headwaters of the creek consist of approximately 1,200 acres (490 ha) of undeveloped canyonlands in the Limestone Canyon Nature Preserve.

[6] The middle section of Agua Chinon Creek flows through a culvert underneath the former El Toro Marine Corps Air Station.

The redevelopment of the air base as Orange County Great Park includes plans to daylight the creek and restore streambank habitat.

[7] This work is proposed to create a wildlife corridor between the Cleveland National Forest and the Laguna Coast wilderness area (Crystal Cove State Park).

[8] Below the Air Base/Great Park the creek continues in a buried channel under the BNSF Railway tracks, Interstate 5 and the Irvine Spectrum Center, and is joined from the left by its main tributary, Borrego Canyon Wash.