Although protected under the Maya Biosphere Reserve, the Mirador Basin’s conservation is threatened by local agriculturalists and cattle ranchers in search of new land. These intrusive settlements are highly threatening to the reserve for the slash and burn method of gaining land from the jungle. Fire is set to the land during the peak of the dry season often causing uncontrollable forest fires. Other threats are major logging, drug trafficking, looting and poaching. 

The Mirador Basin is currently being considered for protection by the Congress of the Republic of Guatemala.  It is proposed as a wilderness area, with limited or no road access. The Mirador Basin Project (a project for archaeological investigation in Northern Petén directed by Idaho State University archaeologist Dr. Hansen), together with several other organizations such as the Global Heritage Fund, Conservation International, and the Association of Friends of the Cultural and Natural Patrimony of Guatemala are working continuously to protect this unique region.