The greatest threat to burrowing owls is habitat destruction  and degradation caused primarily by land development. Despite their protected status, burrowing owls and their burrows are routinely destroyed during the development process.
Burrowing owls are also threatened by agricultural development, the use of pesticides and efforts to eradicate prairie dogs , which live side by side with burrowing owls. This is in addition to natural predation by horned owls, hawks, foxes, badgers and even domestic pets.
Droughts associated with climate change  could pose additional problems for burrowing owls through reduced nest success and greater fire frequency. Meanwhile, declining forage values and crop yields could expand the land used for agriculture purposes, putting pressure on what little native prairie habitat is left for the burrowing owl.