Sonoita River is a river in Arizona. It takes its name from the abandoned Pima mission of the same name. It flows steadily for the first fifteen miles of its westward course, but sinks beneath the sand seven to eight miles before joining the Santa Cruz. This confluence provides water for Tumacácori and Tubac and collects in the marsh lands around San Xavier del Bac in great abundance.

On November 17, 1856, the United States Army established Fort Buchanan along its banks in an effort to control the newly acquired Gadsden Purchase.

In the 1890s several stone artifacts were discovered a few feet beneath the surface near the beginning of the river.