A particular environmental issue on Mendip has been disruption of the underground water flow and the destruction of cave systems.

The Carboniferous Limestone is an important public water resource for much of the surrounding region, including around 500 000 people in the Bristol area. As water consumption has increased rapidly over the last 50 years, so the importance of the Mendip Hills as a source of groundwater has grown.

A major planning study carried out by Somerset County Council in the late 1960s (reported in 1971) highlighted the areas where, in the Water Authorities' view, quarrying would be detrimental to the water supply. In the main Mendip ridge, the only areas falling outside those zones were between Moon's Hill and Whatley Quarries, that between Nunney and Waterlip, a small area around Dulcote, and between Axbridge and Crook Peak. West Mendip is presently covered by Groundwater Protection Areas defined by the Environment Agency.

Groundwater flow in the Carboniferous Limestone is mostly through a network of underground conduits or caves. When quarries intercept these flow systems, firstly water can flood workings and alternatively be diverted by pumping, and in the process cut off the original flow, causing springs to diminish or dry up. As the springs themselves are often used for public water supply, this too can be interrupted. Thirdly, quarrying can cause fissures to become blocked e.g. by blasting vibration dislodging the rocks beyond the quarry void itself or by generating fine material which can be washed into fissures. In addition, the limestone has a significant water storage capacity, both above and below the water table. By removing the rock, quarrying can reduce the storage available in the aquifer.

Claims have been made at various times that Mendip quarrying has affected the flow in the famous thermal springs in Bath, but the evidence appears to be inconclusive.

Stringent limits are placed on activities which could interfere with or contaminate water, for example workings are often not permitted to intercept the water table and if they are, strict regimes of pumping and water disposal are imposed.