In the Chihuauan Desert, grasslands are under extreme threat from conversion to agriculture, which may leave the soils in a condition that would prevent the restoration of grasslands. Invasive species and changing fire regimes are also threats to grasslands and other ecosystems.
Riparian corridors and wetlands have are threatened with clearing or draining, invasive species, and lack of regeneration of riparian corridor trees. Shrublands may be increasing in extent, and are one of the few habitats that is well surveyed for birds in the breeding season. Montane habitats are impacted by drought and increased fires, which can leave them susceptible to insect pest invasions.
In the Tamaulipan Brushlands, the riparian corridor is heavily impacted by clearing, impacted by invasive species, and changing due to altered flood regimes on some rivers. Grasslands are altered due to invasive species, brush encroachment, alteration of fire regimes, climate change, and grazing practices. Thorn scrub is a widely distributed and abundant habitat, including some areas of former riparian corridor and grasslands. Natural wetlands are small in scale and located near rivers. Sabal palm forest has been nearly lost along some rivers including the Rio Grande.
In the Gulf Coast Prairie, clearing of thorn forest and thorn scrub is an issue, as is invasive species. Sea grass beds in the Laguna Madre are damaged by boats, and nesting islands can be impacted by feral or semi-feral animals.