Due to the frequent flooding of Mission San Miguel by the Río Guadalupe, missionary Tomás de Ahumada sought another site located on higher ground.

Additional advantages of the site included the northerly location closer to the Presidio of San Diego, as well as the farming and grazing potential of the river valley below.

[1] Due to its proximity to the Pacific Ocean, El Descanso had been involved in a maritime commerce with ships that traveled along its shores in search of merchandise such as otter fur, salt, tallow, vegetables, and grain.

The adobe was made with local soil, water, clay, and sand; unlike the other missionary complexes of the area, these were mixed with pebbles and crushed shells instead of the usual straw, to make the material tougher.

Animals that inhabited the region included red fox, badger, skunk, coyote, deer, cougar, bobcat, hare, rabbit, squirrel, California quail, rattlesnake, several water snakes, and lizards.

The agricultural production was favored by the humid climate, allowing the cultivation of wheat, barley, and corn, as well as a diversity of fruits and vegetables.

Efforts to preserve and study the remaining traces of Mission El Descanso have been implemented under the auspices of Mexico's National Institute of Anthropology and History (INAH).