In the late 1700's, Spain's control over California was basically a bunch of guys in Mexico City yelling into the wind trying to get people hundreds of miles away to do what they want. California, if taken from either the north by the Russians (or British?) or the east by the Americans was an uncontrolled plot of land that was ripe for imperial grabbing. So, to legitimize its ownership of California, Spain had to have some way to create a presence in the land.
Unlike in East Coast America, where New England was flooded with pilgrims and such from Europe, Spain did not have a large insurgence of Spanish coming into the New World. Thus, the problem was: how can Spain colonize this huge plot of land full of all these native peoples with only a limited number of Spanish? The strategy would eventually becoming a three-tiered approach: presidios, pueblos, and missions.
Presidios: forts where soldiers were housed. Pueblos: grew food for the presidios, which also served the purpose of converting Indians to "civilized men." Missions: the only communities that actually (unexpectedly) succeeded by converting Indians to Catholicism and that were operated by Spanish priests. It was Junipero Serra who would establish a solid missionary system in California.
Serra studied philosophy and theology back in old Spain, and had a hankerin' to do some wild-man conversion and to someday become a martyr. In 1749, he got his chance and left for New Spain to be a missionary. Although he was on orders from Spain, Serra would not see his purpose to be under the state--but rather he saw himself to be on orders from God. So one might say that Spain never really held control of California.
Nevertheless, Serra's establishment of the missions would be the closest thing to Spanish colonization. Missions had multiple functions. Although he pueblos were made to be agricultural centers, the missions would eventually produce more food and house more people. Also, Indians would learn agricultural and industrial skills along with Spanish culture. Traditional culture would be hard-hit, but complete assimilation into an European lifestyle was rare. What resulted was rather a blend of indigenous and Spanish culture, much like the population of the missions.
It was thus these missions, brought on by the work of Junipero Serra, that would effect the cultures and cut Spain into the lives of the native Californians.