The WWF is working with on both sides of the U.S and Mexico borders to reduce soil erosion, and fix the water availability issues by building small low-tech water treatment facilities and by replanting the vegitation.
http://www.worldwildlife.org/places/chihuahuan-desert
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The Chihuahuan Desert Nature Center right now is working on rain water harvesting, and are also planting native plants to the area. If you want to help out email this address [email protected]
http://www.cdri.org/conservation.html
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Protecting Mexico's Flora and Fauna from Fracking, is one of 40 organizations that is made of concerned citizens, that research the negative impacts of fracking, making instructive materials for the public and designing workshops and holding press conferences. The state of Chihuahua in Mexico is the largest state and gives name to the Chihuahuan Desert, the worlds third most important desert in terms of diversity. This organization is lead by David Lauer, Fraking Activist
http://www.globalfrackdown.org/global-frackdown-endorsers/