There are plenty of place names in California that are erroneously thought of as Spanish names, but are Native American in origin. Here's a whole 1916 piece on it:
http://soda.sou.edu/awdata/030731c1.pdf
Just a sampling:
Anacapa (Channel Island, Santa Barbara County)
Aptos (Santa Cruz County)
Arcata (Humboldt County)
Azusa (Los Angeles County)
Cahuenga (Los Angeles County)
Carquinez (Contra Costa County)
Castaic (Los Angeles County)
Cayucos (San Luis Obispo County)
Cholame (San Luis Obispo County)
Chualar (Monterey County)
Coloma (El Dorado County)
Colusa (Colusa County)
Consumnes (Sacramento County)
Cotati (Sonoma County)
Hemet (Riverside County)
Inyo (Inyo County)
Invapah (San Bernardino County)
Jamacha (San Diego County)
Klamath (Siskiyou/Del Norte Counties)
Lompoc (Santa Barbara County)
Malibu (Los Angeles County)
Marin (Marin County)
Modoc (Modoc County)
Mojave (Kern/San Bernardino Counties)
Mokelumne (Sacramento County)
Mono (Mono County)
Morongo (Riverside County)
Napa (Napa County)
Natomas (Sacramento County)
Nipomo (San Luis Obispo County)
Ojai (Ventura County)
Otay (San Diego County)
Pacoima (Los Angeles County)
Petaluma (Sonoma County)
Amongst others. It's pretty much all there in the above link. Many of these Native American names were Hispanicized, since they first came into contact with the Spanish first, giving the illusion that these are Spanish place names instead of Native American.