Prior to joining the Union on September 9, 1850, California was governed at different times by both Spain and Mexico. Today, remains of the Spanish influence can still be seen in the historic Old Mission Dam site at the west entrance of the City. Established in 1779 under the direction of Father Junipero Serra, and built by the Kumeyaay Indians, the dam provided water to the land of Mission de Alcala.
The Spanish parceled this region into land grants and divided the grants among Spanish soldiers in payment for services rendered. Years later, the land was sold to American settlers. George A. Cowles (Kohls), a founding father, was one of the local buyers. Cowles bought 4,000 acres in 1877 to develop his vineyards. He also introduced a number of tree species to this area, such as pomegranate and magnolia trees.
Known as Cowleston, the town was linked to the Cuyamaca Railroad at Cowles Station. A landmark that bears this pioneer's name is Cowles Mountain, at the southwest end of the Santee Valley.
Three years after Cowle's death in 1887, Jennie Cowles married Milton Santee, a realtor and surveyor. In 1891, Jennie Cowles Santee received permission to operate the post office under her husband's name. That same year, Cowleston's first school, Cowles School in the Cowles School District, was built.
In 1893, the community followed her lead and changed the town's name to Santee. The school and the school district also adopted the new town name.