The Cuatro Cienegas basin has been extensively altered in its hydrology by digging canals and groundwater pumping for local and regional agricultural irrigation, and for drinking water (Howeth in litt 24 Jan 2007, Flores-Villela in litt. 25 Jan 2007, Hendrickson in litt. 27 Feb 2007). The western side of the basin is experiencing particularly rapid aquatic habitat loss; Laguna Grande was completely dry in 2006. According to current residents of Cuatro Ciénegas, and Dr. Dean Hendrickson, this was the first time anyone had seen it dry (this encompasses at least 50 years, conservatively) (Howeth in litt 24 Jan 2007).

In 2002, surveys of box turtle sites by a team including Brown (who studied the species 34 years previously) located the marshes where Brown worked in the 1960s. The survey indicates that the species has disappeared from about 40% of its former extent of occurrence, while remaining wetland areas within the area of occurrence have become less suitable (or unsuitable) as habitat for T. coahuila as a result of desiccation and altered vegetation structure (Howeth in litt 24 Jan 2007).

Roads, railroads, pipelines and other infrastructure for industrial, logistic, tourism and recreational purposes have impacted the ecosystem, and some of these environmental impacts continue. In the last decade it is known there has been tourist development, and farming expansion continues (Reuters 2007). Roads and fires have created direct-mortality impacts (Howeth in litt. 24 Jan 2007). There is a potential threat from the global pet trade (at least partly met by captive breeding, see Conservation Actions). Hybridization is not an issue for T. coahuila, in contrast to its sympatric turtle species.