Guatemala is mountainous, except for the south coastal area and the northern vast lowlands of Petén department. Two mountain chains enter Guatemala from west to east, dividing the country into three major regions: the highlands, where the mountains are located; the Pacific coast, south of the mountains; and the Petén region, north of the mountains. All major cities are located in the highlands and Pacific coast regions; by comparison, Petén is sparsely populated. These three regions vary in climate, elevation, and landscape, providing dramatic contrasts between hot and humid tropical lowlands and colder and drier highland peaks. Volcán Tajumulco, at 4,220 meters, is the highest point in Central America.

The rivers are short and shallow in the Pacific vertient, larger and deeper, such as the Polochic which drains in Lake Izabal, Motagua and Sarstún that form the boundary with Belize in the Caribbean and the Gulf of Mexico vertient. The Usumacinta river, which forms the boundary between Chiapas, Mexico and Petén is the largest river of the country, and has La Pasión and San Pedro rivers as its tributaries.

According to Parkswatch and the IUCN, Guatemala is considered the fifth Biodiversity Hot Spot in the world. The country has 14 ecoregions ranging from Mangrove forest (4 species), in both ocean littorals with 5 different ecosystems, Dry forest and Thorn bushes in the Eastern Highlands, Subtropical and Tropical rain forest, Wetlands, Cloud Humid forest in the Verapaz region, Mix and Pine forest in the Highlands.

36.3% or about 3,938,000 hectares of Guatemala is forested (2005). Of this, 49.7% or roughly 1,957,000 hectares is classified as primary forest, the most biodiverse form of forest. including 17 Conifer (Pines, Cypress and the endemic Abies Guatemalensis) species, the most in any Tropical region of the world.

Guatemala has listed 252 wetlands, including 5 lakes, 61 lagoons. 100 rivers, 3 swamps, 6 of those wetlands are of international importance or RAMSAR sites. Tikal National Park, with 11 micro climes in it, was the first mix UNESCO World Heritage Site in the world.

Guatemala has some 1246 known species of amphibians, birds, mammals and reptiles according to figures from the World Conservation Monitoring Centre. Of these, 6.7% are endemic, meaning they exist in no other country, and 8.1% are threatened species. Guatemala is home to at least 8681 species of vascular plants, of which 13.5% are endemic. 5.4% of Guatemala is protected under IUCN categories I-V. Guatemala has the largest percentage of Protected areas in Central America, with a total of 91 protected areas and more than 28% of the territory as a protected area.

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