With respect to the pre-Hispanic period, a hypothesis of late Yaqui arrival in the river valleys is generally supported by the limited archaeological record as well as by colonial chroniclers. Approaches by the Spanish have been recorded since 1532. The first confrontations were with the ill-fated expedition of Diego Martínez de Hurdaide in 1607.
Toward 1610, the Yaqui accepted two Jesuit missionaries: friars Andrés Pérez de Rivas and Tomás Basilio. The Yaqui revolted against the missionary regime, however, and in 1741 a treaty was signed by which they acquired the rights to keep their own customs. Government would only be administered by members of their own group, and they would have total possession of their land as well as the right to retain their weapons. In 1767 the expulsion of the Jesuits brought the end of the relative peace the Yaqui had so far enjoyed and placed the communities under Franciscan governance. As a result, the Yaqui lost more territory to the colonists. By 1825, the Yaqui rebellion had begun. It would later mark the course of the relationship between the Yaqui and the subsequent regimes of the Mexican Republic. This period is often referred to as the "Wars of the Yaqui." It resulted in a drastic population loss and political imbalance, conditions that permitted the oligarchy, to continue colonizing the entire valley.
The genocidal offensive was intensified during Porfirio Diaz's rule, and thousands of Yaqui were expelled to Yucatán and Quintana Roo to be sold as slaves. Hundreds looked for refuge in Arizona, in the United States, where they have lived ever since in the towns of Pascua, Guadalupe, and Barrio Libre. The Yaqui participation in the revolutionary conflict was based on the promise by General Alvaro Obregón to return their land. The promise was not fulfilled, and a new revolt started. It lasted until the end of 1929, when President Emilio Portes Gil signed a peace agreement with the Yaqui that forced them to live under supervision by the army until 1936.
Through the agreements reached with President Lázaro Cárdenas, 485,235 hectares of land were ratified and acknowledged as exclusive Yaqui territory. Armed confrontations came to an end, and a period of reintegration began, during which several thousand Yaqui returned to their territories. In 1940 irrigation district no. 18 was created, and new plans for agricultural development arose. Owing to the construction of several dams, the river, a resource indispensable for production, was lost.