While Spain's effort to claim California, Mexico, and other vast lands as its holdings was mostly considered a power play by a country far away, the brave men known as Padres, Freres or Fathers who were assigned and delivered to these shores with cattle, food stocks, vines & plants, their clothing and books, were the true foot soldiers for the Spanish government. They introduced Christianity to the California coast, and not all the local populations welcomed their message or arrival.
When forced to depart in the early 1800's as Mexico gained its independence from Spain and took control of mission lands in "Alta California," there were 21 missions without masters. Most fell into disrepair.
The effort by the Spaniards to utilize Indian populations as labor to make the missions thrive and become self-sustaining city centers, was met with obstacles. Native men often considered farming a form of labor beneath them and were opposed to growing food on farms. Thus, the Spanish missionaries were not generally well received by local populations. But many natives did relinquish and accept these newcomers and their religion in trade for a steady supply of food and modern convenience such as running water in aqueducts, wines and cattle brought from Spain to supply milk, meat, etc.
It's hard to say what kind of impact the new Christian religion and way of life had in the long term. Thousands of Indians died from diseases brought by these foreign travelers and many native populations were almost completely lost to smallpox and other such illnesses introduced.
The very formation of the mission system was fraught with challenge, in fact. The first Christian martyr for Spain had been assigned by Fr. Junipero Serra to stay in San Diego and build the first mission. When 800 American Indians stormed onto the grounds in the middle of the night on November 4th, 1775, they pillaged the mission, burned it to the ground and massacred Father Jayme. He was buried under the altar in the present church and took his place in history as the first Christian martyr in California. Father Serra returned to Mission San Diego de Alcala to oversee the rebuilding of the mission. Fearing there would be another raid, the padres rebuilt the mission according to the specifications of an army fort.
You can visit the mission today and even attend church services. Like the majority of missions in California that have been rebuilt as time, earthquakes, fires and other forces caused the buildings to crumble, Mission San Diego acts both as a museum where scholars and students study California history, and as a church. This icon for local history remains a house of worship for Christianity that the missionaries introduced.