Recruits were largely drawn from the Californio population (colloquially known as "Native Californians"), though its ranks included Yaqui and Mission Indians as well as immigrants from Mexico, Hispano America and Europe (particularly France).

Because of its somewhat swampy location on the banks of the Santa Cruz River, the men suffered from an epidemic which at one point rendered over half of them too sick for duty and resulted in 8 deaths, including two of the Battalion's officers.

These conditions brought the construction of permanent buildings at the post to a halt, forcing the men to live in tents and temporary brush shelters during their service there and generally curtailing operations against the Apaches.

Shortly after their arrival at Fort Mason, Captain Pico led a detachment across the border to Magdalena, Sonora in an unsuccessful effort to recapture deserters being held by Imperialist forces there.

In November, 1865, in response to a cross-border incursion at the settlement of San Rafael by Col. Refugio Tánori and some 350 Opata militia loyal to the Imperialists, a force of Native Cavalrymen pursued the raiders as far south as Ímuris, Sonora.