Cuenca Los Ojos was founded in the 1990s with the mission of preserving and restoring the monumental habitat of the Madrean Archipelago and protecting the vast number of species it supports. Through collaboration between environmental groups and governmental agencies, more than a million acres have been protected in the ecoregion. At the center of this conservation area are the lands of CLO, with over 130,000 acres in Mexico alone. They form the liaison between the USA and Mexico and secure a vital piece of the greater continental migratory route that extends along the western spine of the North and South American Continents.

The restoration of key habitats has been achieved though the construction of thousands of small rock dams, berms, and gabions in eroded areas. CLO has also worked to remove exotic species, aerate soils, apply seeding and manage grasslands through controlled burns and fallowing. As a result of CLO's restoration work, water tables in the San Bernadino Ranch have risen 30 feet in the middle of a 15-year drought and at least 15% of the historic wetland has been restored with six miles of river now flowing year round. Moreover, more than 5,000 acres of grasslands have been aerated and reseeded. Restoring habitat has been key to bring back native wildlife populations such as Coues deers, Black bears and Gould’s turkeys.