The reservation was created by US Executive Order in 1875 for local Kumeyaay people. Its name comes from the Spanish Coapan, which was what the area west of the San Diego River was called in the 19th century. The dry, mountainous and chaparral lands proved inhospitable.
In the early 20th century, the state of California first created Lake Cuyamaca on the reservation, which provided water for growing San Diego. Then in 1931, the state flooded the heart of the reservation, creating the El Capitan Reservoir. Many Kumeyaay families had homes in the floodzone, and they petitioned Congress to prevent the loss of their land; however, Congress gave San Diego the right to buy the land without the local Kumeyaays' knowledge or consent. The two tribes, Barona and Viejas, were forced to sell the land and with their proceeds they purchased their current reservations, the Barona Reservation and Viejas Reservation, respectively.