The Cuatro Ciénegas Valley is a protected area that contains numerous hot and cold pools with varying salinity and hosts a large variety of endemic species, from stromatolites to algae and birds. Human activities threaten to consume the water resources and the abundant gypsum outcrops that support endemic vegetation species. The research results showed that significant changes, as reduction of up to 80% in the size of the pools, occurred in the study area as well as a decrease in the gypsum-covered areas. The changes are mostly related to human activities, as farming and mining that cause overexploitation of the aquifers and unregulated gypsum exploitation. The conservation plans of the ecosystem in this special area must take into account the change rate in the land cover and pools size in order to regulate land use and aquifer exploitation.