The buildings of the complex were made of adobe, with round stone foundations, set at a depth of 90 cm, cemented with a mortar of clay, sand, and lime.

The adobe bricks resting on the foundation were cemented with the same mortar and placed in an alternating fashion to give the structure more strength and stability, making walls from 0.9 to 1.1 m thick.

Further downhill this stream joins the sea, forming an estuary rich in diverse types of plants and animals, such as white herons and wild ducks.

The missionaries wrote in their diaries about finding plentiful pasture in the area and further inland as well as watercress, chia, mangrove, cattail, brushwood, a few isolated pines, yucca, mesquite, sycamores, chamomile, willows, and evergreen oaks.

Conservation efforts at San Miguel form part of the "Camino Real Misionero de las Californias" program of Mexico's National Institute of Anthropology and History (INAH).

The remains of the walls are covered by a layer made of clay, sand, water, slices of nopal cactus, and manure to protect them from the wind, sunlight, and rain.