The Maya lowlands are the most complex area in terms of geographical features, due to its large size and high biodiversity. In general, the region is defined by having an altitude of less than 300 m, with the exception of the Maya Mountains and the Sierra de Puuc, where higher elevations can be found. Geologically, the lowlands are composed of metamorphic mantle composed mainly of limestone, which has been constantly modified by the action of water, earthquakes, and other forms of erosion. For geographical and cultural purposes, it is appropriate to distinguish which are the Central Lowlands and the Northern Lowlands, experiencing very particular features, although each of these two areas also have their own micro-regions.

The Central Lowland constitute what is known as Petén, and includes what is now the Department of Petén, Belize, southern Campeche and Quintana Roo and the eastern part of Tabasco and Chiapas. Peripheral regions as the basin of the Usumacinta River, the Copán Valley and the Gulf of Honduras may present some features of the Highlands. The vegetation of Petén is characterized by forests that exceed the 40 m high, and rainfall is high, especially between the months of July and January. The fertile soils are in flood-prone areas and in general tend to be shallow, limiting the extensive agriculture. The presence of some permanent water sources such as rivers Usumacinta, Grijalva, San Pedro, Candelaria, La Pasión, Belize and Hondo; lakes like Petén Itzá and Izabal; and the lagoons of Térrminos, Yaxha and Bacalar.

The Northern Lowlands present a different picture, with drier weather and lower forests. They are also quite important coastal and wetland-rich mangrove forests, salt deposits and various marine products areas. Despite having constraints to agricultural production, the region of the Lowlands is characterized by the development of the largest and most complex cities, which could reach up to 100,000 people. Decades of environmental and agricultural studies have determined that this was possible thanks to the combination of different systems of intensive agriculture and hydraulic steering and dispersed design of residential areas surrounding the ceremonial centers. In addition, the key factor was the uptake of water in many areas that do not have permanent water sources. For this reason many settlements were located near lakes and low seasonal flooding, and watery or reservoirs were built in major cities. To the north, the settlement took the cenotes, which are the only sources of water inland. Tanks were also built into the limestone, which are known as chultunes.