The Mendip Hills are the most southerly Carboniferous Limestone upland in Britain. Carboniferous Limestones were laid down during the early Carboniferous period, about 320–350 million years ago. Subsequently, much of northwestern Europe underwent continental collision throughout the late Paleozoic era, culminating in the final phases of the Variscan orogeny near the end of the Carboniferous period, 300 million years ago. This tectonic activity produced a complex suite of mountain and hill ranges across what is now southern Ireland, south-western England, Brittany, and elsewhere in western Europe.

As a result of the Variscan mountain-building, the Mendip area now comprises at least four anticlinal fold structures, with an east-west trend, each with a core of older Devonian sandstone and Silurian volcanic rocks. The latter are quarried for use in road construction and as a concrete aggregate. Mendip was considerably higher and steeper 200 to 300 million years ago, since when weathering has resulted in a range of surface features including gorges, dry valleys, screes and swallets. These are complemented underground by a large number of caves, including Wookey Hole, both beneath the plateau and at the base of the southern escarpment. There are also limestone pavements and other karst features. Dissolution of the limestone produced many of the gorges including, most famously, Cheddar Gorge and Burrington Combe. Springs, a number of which deposit tufa, are a particular feature of the eastern part of the hills.

The Devonian and Silurian rocks are generally more resistant to weathering than the limestone, and form some of the highest points on the hills, including the highest at Beacon Batch on Black Down, 325 metres above sea level. Black Down is a moorland area, with its steeper slopes covered in bracken and its flatter summit in heather and grasses rather than the pasture which covers much of the plateau. The main body of the range is an extended plateau, 4 to 5 miles wide and generally about 240 metres above sea level.

In some areas the Carboniferous Limestone and the dolomitic conglomerate have been mineralised with lead and zinc ores. From the time of Roman Britain until 1908, the hills were an important source of lead. These areas were the centre of a major mining industry in the past and this is reflected in areas of contaminated rough ground known locally as "gruffy". The word "gruffy" is thought to derive from the grooves that were formed where the lead ore was extracted from veins near the surface. Other commodities obtained included calamine, manganese, iron, copper and baryte. The eastern area reaches into parts of the Somerset Coalfield.

North and east of Mendip, the same Carboniferous Limestone layers are found in the subsurface and are exposed in Avon Gorge, but younger strata overlie the Carboniferous Limestone in Dundry Hill and the Cotswolds, where oolitic limestone of Jurassic age is found at the surface. West of the main Mendip plateau the Carboniferous Limestone continues in Bleadon Hill and Brean Down, and on the islands of Steep Holm and Flat Holm.