The Serra Geral do Tocantins Ecological Station is in the Cerrado biome. It covers an area of. It covers part of the Formosa do Rio Preto municipality of Bahia and the Almas, Mateiros, Ponte Alta do Tocantins and Rio da Conceição municipalities of Tocantins. The ecological station is one of the largest in the country, and covers an area with one of the lowest population densities in the country. The terrain has a series of levels with gently undulating relief, with escarpments forming plateaus typical of an area of sedimentary deposits. Altitudes range from. The unit lies on the divide between the Tocantins-Araguaia basin and the São Francisco basin. Most of it is in the Tocantins-Araguaia basin, which drains the north, south and west parts in the Tocantins municipalities. The Balsas, Novo, Ponte Alta and Manoel Alves rivers are in this basin. The São Francisco basin drains part of the east of the unit in Bahia, and includes the Sapão River, a tributary of the Preto River of Bahia. The unit is above the Urucuia aquifer, a major freshwater storage site consisting mainly of sandstone. Rainfall is annually. Average annual rainfall is. Temperatures range from with an average of. The climate is hot and dry in the period from May to September, with large swings in temperature between night and day, when temperatures may reach. The rainy season lasts from October to April.
Flora
Vegetation is 81% grassland, 17% savannah and 1% forest. The remainder is covered by introduced flora. 417 plant species have been recorded in 89 families and 204 genera, including the threatened Myracrodruon urundeuva. A type of Ochnaceae found occasionally in Campo Sujo areas near Morro do Fumo may be a new species. Some areas hold the "golden grass" capim-dourado and the Buriti palm, species that suffer from great extractive pressure in the microregion of Jalapão.
The local population is generally very poor, depending on subsistence farming and cattle raising, and the sale of golden grass. Due to the irregular land ownership situation, as of 2005 the area suffered badly from illegal burning to create new pasturage for cattle. Burning is also done due to a local belief that it is needed by the golden grass, used in handicrafts. From May to October there is hardly any rain, and there is a high risk of fire. Natural fires caused by lightning would have occurred in early summer, followed by rain, so would have been small and of short duration. Man-made fires occur later in the season when the vegetation is drier and there is more wind, so last longer and cover larger areas. This occurs during the breeding season of most birds, who typically next on the ground or within of the ground. The frequent fires also reduce available food supplies for the fauna including small animals and the birds of prey that depend on them. Paving of highways in the area and the connections between Ponte Alta, Porto Nacional and Palmas have attracted squatters who plant one or two crops, then make pasture for cattle. The arrival of soybean farmers has caused new environmental problems since the soil is very fragile. There are no sewage treatment plants in the municipalities, so sewage is polluting the water table. Garbage dumps created by the inhabitants and litter from visitors are also a problem.