The name Capitan Grande derives from the Spanish coapan, a word referring to the area west of the San Diego River. By 1875, when President Grant's executive order created the reservation, the Kumeyaay people who had lived in the region for thousands of years had already experienced decades of mission domination, Mexican land grant displacement, and American squatter encroachment. The reservation was an attempt to secure some land for the people who had been on all of it. What was set aside — 15,753 acres in the Cuyamaca Mountains and Cleveland National Forest — was rugged and dry, terrain that the surrounding settlers had not found useful enough to claim. This is a pattern in the history of American Indian reservations: what was offered was what no one else wanted.

El Capitan Reservoir was created by El Capitan Dam, completed in 1934, though the reservoir began filling earlier. The San Diego County Water Authority needed water storage to serve a rapidly growing population, and the San Diego River's upper watershed, including the valley bottom of the Capitan Grande Reservation, was the chosen site. The Barona and Viejas groups were not asked whether this arrangement was acceptable. They were offered money for the land that would be submerged. They took it — there was no mechanism by which they could refuse — and used the funds to purchase their current reservations: Barona north of Lakeside in Wildcat Canyon, Viejas to the south. Both tribes relocated in the early 1930s, leaving Capitan Grande empty.

The remaining Capitan Grande Reservation land — the portions the reservoir did not flood — is uninhabited chaparral and mountain terrain in the Cleveland National Forest. The Barona and Viejas tribes hold a joint-trust patent on this land, meaning they share ownership of the remnant reservation that neither tribe occupies. The terrain is steep, dry, and rocky: the kind of landscape that is genuinely difficult to live on, which is part of why it was not flooded and part of why the two groups were moved off the valley land rather than retreating to the mountain margins. The land exists in legal limbo — held, but not inhabited; owned, but not used in the conventional sense.

The Barona and Viejas tribes rebuilt on their new reservations. The Barona Group established the Barona Resort and Casino in Wildcat Canyon, eventually becoming one of San Diego County's major gaming operations and the home of the Blackjack Hall of Fame. The Viejas Band developed the Viejas Casino and Outlets south of Alpine. Both tribes leveraged the sovereignty that their federal recognition protected — sovereignty that had not prevented the state from flooding their original reservation, but that later provided the legal basis for gaming operations the state could not prohibit. The El Capitan Reservoir still supplies water to San Diego. The Capitan Grande Reservation still sits in the mountains above it, uninhabited and jointly held, a geographic record of what California water policy cost.