Uttarakhand has a total geographic area of 51,125 km², of which 93% is mountainous and 64% is covered by forest. Most of the northern parts of the state are part of Greater Himalaya ranges, covered by the high Himalayan peaks and glaciers, while the lower foothills were densely forested till denuded by the British log merchants and later, after independence, by forest contractors. Recent efforts in reforestation, however, have been successful in restoring the situation to some extent. The unique Himalayan ecosystem plays host to a large number of animals (including bharal, snow leopards, leopards and tigers), plants and rare herbs. Two of India's mightiest rivers, the Ganges and the Yamuna take birth in the glaciers of Uttarakhand, and are fed by myriad lakes, glacial melts and streams in the region.

Uttarakhand lies on the southern slope of the Himalaya range, and the climate and vegetation vary greatly with elevation, from glaciers at the highest elevations to subtropical forests at the lower elevations. The highest elevations are covered by ice and bare rock. Below them, between 3,000 and 5,000 metres (9,800 and 16,000 ft) are montane grasslands and shrublands: the western Himalayan alpine shrub and meadows. Temperate coniferous forests, the western Himalayan subalpine conifer forests, grow just below the tree line. At 3,000 to 2,600 metres (9,800 to 8,500 ft) elevation they transition to the temperate western Himalayan broadleaf forests, which lie in a belt from 2,600 to 1,500 metres (8,500 to 4,900 ft) elevation. Below 1,500 metres (4,900 ft) elevation lie the Himalayan subtropical pine forests. The Upper Gangetic Plains moist deciduous forests and the drier Terai-Duar savanna and grasslands cover the lowlands along the Uttar Pradesh border. This belt is locally known as Bhabhar. These lowland forests have mostly been cleared for agriculture, but a few pockets remain.

Indian National Parks in Uttarakhand include the Jim Corbett National Park (the oldest national park of India) at Ramnagar in Nainital District, Valley of Flowers National Park and Nanda Devi National Park in Chamoli District, which together are a UNESCO World Heritage Site, Rajaji National Park in Haridwar District, and Govind Pashu Vihar National Park and Gangotri National Park in Uttarkashi District.