Alfred Kroeber noted that the name may be derived from the Luiseño word temet meaning "sun".

The Santa Margarita River begins at the confluence of the two creeks at the head of Temecula Canyon.

[citation needed] Biologically diverse, supporting both coastal and desert fauna and flora, it is bounded by the Agua Tibia Wilderness area and the Cleveland National Forest.

The creek supports coastal sage scrub, including Jojoba, alluvial fan scrub, mesquite bosque mix, coast live oak woodland, and mature Fremont cottonwood-willow woodland.

[9] North American beaver (Castor canadensis) may gradually raise the water table and return portions of the stream to perennial flow at sites such as its confluence with Murrieta Creek.