Naachtún Dos Lagunas Biotope is located in the northeast corner of the department of Petén and the Maya Biosphere Reserve. The biotope is under the jurisdiction of the municipality of Flores, but he legal area of the biotope is not totally clear. According to the Center of Conservation Studies (CECON), the biotope's area is 49,500 ha (CECON 1996), while Guatemala's National Council of Protected Areas (CONAP) considers its area to be only 30,179 ha (CONAP 1999). The reason for the confusion is that upon the biotope's creation, its legal coordinates did not match its area. As a result, maps have been drawn showing the southern border slanting diagonally in a northeast-southeast trajectory. According to Barrios (2002, pers. comm.), the problem originated when the biotope's coordinates were transcribed incorrectly. This error has decreased the area of the biotope and CECON is currently correcting the problem.
The biotope shares physical and biological characteristics with a large zone that extends towards the east and west of the biotope into El Mirador-Río Azul National Park; towards the south, in the Multiple Use Zone of the MBR of Guatemala; and towards the north, in Mexico's Calakmul Biosphere Reserve.
Naachtún Dos Lagunas is part of the physiographic region called the Yucatán Platform. The platform is characterized by karstic topography with steep, rounded hills alternating with lowland depressions. The soils are composed of residual clays that have low permeability and fertility, and are shallow and easily eroded (CECON 1996). In those areas with steep slopes, or in flat areas with porous soils, drainage is very rapid. This characteristic may be the reason why the vegetation loses part of its leaves during the dry season (Pennington and Sarukhán 1998). Using the classification system of Dinerstein et al. (1995) as a reference, the ecoregion of the biotope is the Tehuantepec Moist Forest.
The altitude varies between 100 to 300 m, and the average annual temperature is 25º C. According to data from Tikal's meteorological station (the closest to the area), the range of temperatures oscillates between 20º C and 30.7º C. The annual average precipitation ranges from 1,160 and 1,700 mm, with a three-month dry season between February and May (CECON 1996).
The area's archeological wealth is outstanding, having valuable Mayan remains (CECON 1996). Part of the biotope's name comes from one of its archeological sites - Naachtún. This site has three structures and one observatory in the northern plaza, 21 sculpted stelae, 24 smooth stelae, and nine altars. The most important archaeological investigations were done on these sites between 1922 and 1943 (IDAEH 1999).