The Santa Gertrudis site is classified as interior mountain mid-peninsula oasis,[3] and is considered to be on the smaller side[4] relative to the 183 other identified oases on the Baja California peninsula.

[5] Baja has no perennial rivers so what mesic habitats exist are "small riparian environments"[3] sustained wholly by springs, seeps, human-mediated oases, wetlands, and seasonal ponds (pozas or tinajas).

[6] Biologists from San Diego State University who visited the site in 1990 described it as "thickly vegetated, wide, funnel-shaped, rocky arroyo which narrows at its eastern end at the western foot of the Sierra Santa Agueda [d]".

[8] However, the site continually imported staple foods, including "flour, corn, beans, rice, chick-pea, lentil, sugar,"[5] and hunting (deer) and foraging (hearts of agave) remained a major source of calories for residents of the settlement.

[7] Other plants present in the system include acacia, banana, fig, guava, mango, mulberry, pomegranate, prickly pear, olive, tamarind, tepeguaje, and white sapote.

[11] According to ethnobotanists Rafael de Grenade and Gary Paul Nabhan, the Baja mission oasis ecosystems generally support local biodiversity through "highly interactive, though not truly mutualistic relationships...providing food resources to temporary and permanent resident species, ecosystem structure for nesting and habitat sites, shade for understory species and organic matter that alters soil composition and moisture.

Grapevines, pomegranate bushes and fig trees as understory introduced species also provide food and habitat resources as well as contribute to the agroecosystem structure and function.