The valley takes its name from the Kumeyaay village of San Pasqual, which existed here long before the missions arrived. When the Mexican government ended the mission system in 1833, the Kumeyaay who had been drawn into mission life moved back to San Pasqual Valley, and on November 16, 1835, under territorial governor José Figueroa, the pueblo of San Pasqual was formally established.

For over four decades the Kumeyaay worked the valley — farming, raising animals, defending against raids from other bands, navigating the political complexities of Mexican California and then the American conquest. Their leader Jose Pedro Panto was resourceful enough that both Mexican ranchers and American settlers sought to leverage his authority for their own purposes. In 1878, San Diego County authorities evicted the Kumeyaay from their homes. The original reservation established for them in 1910 became, eventually, the site of the Safari Park. The San Pasqual Band of Diegueno Mission Indians now lives on a reservation near Valley Center, a few miles north.

On December 6, 1846, General Stephen Kearny's Army of the West rode into the valley and met General Andres Pico's Californio lancers. The result was the bloodiest engagement of the Mexican-American War in California: seventeen Americans killed, eighteen wounded, Kearny himself injured, the survivors retreating to a small rise they occupied until December 11, eating their mules to survive. The Californios won the day. The Americans won the broader war, and California became a territory of the United States.

The San Pasqual Battlefield State Historic Park, 50 acres on Highway 78 adjacent to the Safari Park, marks the site. Living history presentations are held there by volunteers who portray both sides of the battle — the dragoons and the lancers, and sometimes the Kumeyaay who watched both from the valley they had farmed for decades.

Agriculture in San Pasqual Valley has always followed the land's character: hot days, ocean-cooled nights, good soil in the bottomlands, and water that requires management rather than being taken for granted. The Kumeyaay farmed here. The Mexican ranchers raised cattle. The American settlers planted citrus and avocados.

In 1981, San Pasqual Valley became the fourth wine region in the country to receive an American Viticultural Area designation — a recognition that the valley's climate and terrain are distinctive enough to produce wines worth labeling by origin. The warm, dry conditions favor Rhône varieties: Syrah, Mourvedre, Viognier, along with Merlot and various Italian and Spanish grapes. The oceanic influence, channeled through the valley from the Pacific thirty miles west, provides the cooling that makes grape cultivation viable. Several working wineries operate in the valley alongside the dairy farms and avocado groves and the Zoo's 1,800-acre compound.

San Pasqual Valley is the northernmost community of San Diego, a designation that understates how much it has been shaped by events that happened here rather than in the city it technically belongs to. The Santa Ysabel Creek watershed drains through it into the San Dieguito River. State Highway 78 connects it to Escondido on the west and Ramona on the east. In between, the valley floor holds more history per square mile than most places in California think to carry.

The Safari Park alone draws enormous numbers of visitors who may not know they are driving through the site of an 1846 battlefield, across land that was farmed by Kumeyaay people for centuries before any of the Anglo institutions that surround them existed. The valley does not announce its complexity — it is a pleasant drive between hills. But the layers are there for anyone who wants to look.