The municipality covers an area of 441761.2 ha of which 78.4 % has remained as natural habitat. There are no RAMSAR sites in the municipality. There are four formal land-based protected areas. These include the Golden Gate Highlands National Park which comprises of 23444.1 ha (5.31 % of the municipal area) and the Sterkfontein Dam Nature Reserve which comprises of 18489.9ha (4.19% of municipality).

There is one biome in the Maluti-a-Phofung Municipality, namely Grassland. Twelve vegetation types cover 441 761 ha of the municipality. These are Basotho MontaneShrubland, Drakensberg Afroalpine Heathland, Drakensberg-AmatholeAfromontaneFynbos, Eastern Free State Clay Grassland, Eastern Free State Sandy Grassland, Eastern Temperate Freshwater Wetlands, Lesotho Highland Basalt Grassland, Low Escarpment Moist Grassland, Northern Afrotemperate Forest, Northern Drakensberg Highland Grassland, Northern Free State Shrubland and uKhahlamba Basalt Grassland.

There are also three vulnerable ecosystems, covering 798.5 ha of the Maluti-a-Phofung Local Municipality. This is the Eastern Free State Clay Grassland, Eastern Temperate Freshwater Wetlands and the Low Escarpment Mistbelt Forest. The Freshwater Ecosystems in the municipality are characterized by four water management areas including Thukela, the Upper Orange and the Upper Vaal. Fifteen rivers run through the municipality, including the Caledon, Elands, Fraserspruit, Klerkspruit, Klip, Liebenbergsvlei, Liqobong, Little Caledon, Meul, Nuwejaarspruit, Thukela, Tierkloof, Vaalbankspruit and Wilge. Wetlands cover 14762.3ha of the municipality.

• MAP Environmental Policy
• SEMP MAP
• Wetland Assessment Reports, November 2010