The potential mission site was identified in 1794 by a military party led by Sergeant José Manuel Ruiz and accompanied by missionary Tomás Valdellón.

Still other accounts maintain that the uprising that destroyed the mission included not only the Kiliwa but also the Paipai, Kumeyaay from La Huerta, and Colorado River groups such as the Quechan and Cocopa as well: They were without a leader in the attack; all fought like animals.

(Meigs 1935:123) Thereafter, the Kiliwa renamed Santa Catarina Wa'iú-ichíu, a combination of the words wa (house), iú (empty), and ichíu (burned).

In 1855, the Mexican government granted ownership of the lands of the ex-mission of Santa Catarina to General Ricardo Palacio for his patriotic service to the nation.

Valdellón reported in 1797 that the Santa Catarina capilla (chapel) was constructed of adobe bricks and measured 10 × 5 m, and featured a flat roof; it housed a 150 cm tall statue of Saint Catherine of Alexandria.

As agriculture was fundamental for the subsistence of the site, mission industries consisted mainly of the cultivation of wheat and maize, and the raising and trading of cattle, donkeys, goats, horses, mules, and sheep.

The nearby rancherías of Agua Caliente, Agua Caliente del Portezuelo, Cerro Colorado, El Portezuelo, El Rincón, La Ciénega, La Huerta, Los Bateques, Poza de González, San Pablo, and Sangre de Cristo were integrated into the Mission holdings.

The following account of Santa Catarina's resident priests is based on the President of the Missions' nómina sacra, or chart of "sacred names":