Naatchún Dos Lagunas was declared a protected biotope in 1989 with the Decree 4-89 (Guatemala 1989) and by means of the declaration of the Maya Biosphere Reserve in 1990. It constitutes one of the core areas of the MBR, in addition to El Mirador-Río Azul, Tikal, Laguna del Tigre, and Sierra del Lacandón National Parks, and San Miguel La Palotada El Zotz and laguna del Tigre Protected Biotopes. Naachtún Dos Lagunas is administered by CECON, which is part of the Faculty of Chemical Sciences and Pharmacy of the San Carlos University of Guatemala (USAC)--an autonomous governmental institution. In addition, by law, CONAP shares administrative duties of the area with CECON. The biotope does not have a management plan but operative plans are prepared annually. These plans include subprograms in the areas of administration, construction, environmental education, interpretation, and research. The area is considered a conservation priority by CECON, and according to the 2000 operational plan, the primary objectives for the biotope are to promote protective mechanisms for the natural environment; to develop programs that support the conservation of biological diversity; to strengthen measures to preserve archaeological, historic, and cultural features; to foment and support the development of projects in scientific research; to increase educational programs in conservation within the area as well as in the surrounding zone of influence; and to promote and support activities related to cultural and ecological tourism.

The only active programs in the biotope are vigilance and maintenance activities, and there is no evaluation of their effectiveness. There is one scientific station where formal research programs are being developed. The main activities that occur in the biotope are the exploitation of forest resources, and some tourism and research. Those resources that are exploited by the nearest communities are xate, pepper, chicle, mimbre, and various medicinal plants (Ramos 2002, pers. comm.).

In 2000 the USAC donated about $34,600 for the biotope's budget. The funds were distributed for salaries, travel expenses, transportation, management infrastructure and training, and prevention of forest fires (CECON 2000). In the same year, the MacArthur Foundation gave a NGO a donation to support the operation of the biotope; however, the funds were misappropriated and USAC took over management of the funding (Barrios 2000). For 2002, the biotope enjoys relatively solid financial support compared to previous years; however, it remains seriously underfunded. This year's funding will be invested in infrastructure for personnel ($6,500), salaries ($2,000), and the purchase of mules (to carry equipment), vehicles, and fuel ($5,200).

The biotope has eight park guards, one technician, and an administrator, who is the regional representative of CECON. The technician and the administrator also work in three other areas admnistered by CECON: Laguna del Tigre, El Zotz, and Cerro Cahuí Biotopes. Park guards work for twenty-two days each month, with eight days of vacation. Each park guard works one year at Naachtún Dos Lagunas before being transferred to one of the other biotopes mentioned above. CECON guards are assisted in their patrolling by CONAP park guards from the El Cedro guard station. According to the biotope's administrators, despite CONAP's assistance, the current number of personnel is not sufficient to adequately patrol the entire biotope. One problem is the work/vacation structure which often leaves only two park guards working at one time (Barrios 2002), and are only able to make short patrols close to the base camps. Administrators estimate that eight more people are needed to ensure effective vigilance of the entire biotope (Barrios 2002).

The geographic coordinates according to CECON should be P1: 17° 48' 52" / 89° 46' 07;" P2: 17° 48' 52"/ 89° 30' 05;" P3: 17° 40' 00"/ 89° 30' 05;" and P4 : 17° 40' 00"/ 89° 46' 07." According to CONAP, the P4 limits should be: 17° 46' 00"/ 89° 46' 07." The legal boundaries are not demarcated, except for the northern limit where a wide gap is clearly defined and marks the border between Mexico and Guatemala (controlled by the army). The other boundaries have not been demarcated, including the east and west boundary with El Mirador-Río Azul National Park, and the southern boundary with the Multiple Use Zone of the MBR along the forest concession belonging to the community of Uaxactún.