The central Cairngorms contain the extensive high-level plateaux that are bordered by vertical cliffs and deep corries. The summits and plateaux support important alpine and arctic habitats. These include the three-leaved rush and Rhacomitrium heaths, which are the most extensive in Britain and are fragile and sensitive to disturbance by people and grazing animals. The more sheltered snow bed communities include many rare and specialised mosses and liverworts. The mountain vegetation supports a wide range of specialised and rare invertebrate and vertebrate animals. Specialised birds include the dotterel, snow bunting and ptarmigan.

Dwarf-shrub heaths grade from the high elevation wind-clipped heaths to the lower slopes that are dominated by deep heather. Blanket bogs occupy suitable sites and extend to higher elevations in the Cairngorms than elsewhere in Britain. Cliffs and rock outcrops that are inaccessible to deer and sheep support habitats that are very sensitive to grazing impacts. These include tall herb communities, arctic-alpine plants and montane scrub. The lower elevations are dominated by moorlands with dry heather dominated heaths and wetter heaths and blanket bogs. Many of these habitats are maintained by heather burning and grazing, without which they would revert to woodlands.

On the lowest slopes woodlands are dominant. These include the largest native pine forests in Scotland and significant areas of non-native forests. The forests support capercaillie, crested tit, Scottish crossbill, black grouse, red squirrel, pine marten, juniper and a range of scarce vascular and non-vascular plants. In the absence of muirburn and with low levels of grazing, forests would expand onto higher elevations forming wind-blasted tree lines.

Freshwater and related habitats are important in the Cairngorms and there are concerns over the conservation of Atlantic salmon, freshwater pearl mussel, otter and water vole. Appropriate levels of grazing can help to maintain riparian habitats, but heavy grazing on the banks of watercourses and lochs can have detrimental impacts on riparian plant communities and their associated fauna.

Farming is an important commercial activity, especially on the low in-bye ground and grazing by deer can cause additional impacts to agricultural land.