The caves have been used by humans for around 45,000 years, demonstrated by the discovery of tools from the Palaeolithic period, along with fossilised animal remains.

The show cave consists of a dry gallery connecting three large chambers, the first of which contains the Witch of Wookey formation.

[7][8] The river is maintained at an artificially high level and falls a couple of metres when a sluice is lowered to allow access to the fourth and fifth chambers, two small air spaces.

[12] Some of the water is allogenic in origin i.e. drained off non-limestone rocks, collecting as streams on the surface before sinking at or near the Lower Limestone Shale — Black Rock Limestone boundary, often through swallets such as Plantation Swallet near St Cuthbert's lead works between the Hunter's Lodge Inn and Priddy Pools.

[13] It then passes through major cave systems such as Swildon's Hole, Eastwater Cavern and St Cuthbert's Swallet, around Priddy,[14][15] but 95% is autogenic water that has percolated directly into the limestone.

[15] The southern slopes of the Mendip Hills largely follow the flanks of an anticline, a fold in the rock that is convex upwards and has its oldest beds at its core.

[16] The outer slopes are mainly of Carboniferous Limestone, with Devonian age Old Red Sandstone exposed as an inlier at the centre.

Wookey Hole is a solutional cave, mainly formed in the limestone by chemical weathering whereby naturally acidic groundwater dissolves the carbonate rocks, but it is unique in that the first part of the cave is formed in Triassic Dolomitic Conglomerate, a well-cemented fossil limestone scree representing the infill of a Triassic valley.

[19] The current resurgence is located close to the base of the Dolomitic Conglomerate at the head of a short gorge formed by headward erosion with subsequent cavern collapse.

The streamway in the outer part of the cave system that is formed within the Dolomitic Conglomerate is characterised by shallow loops linking low bedding chambers, or tall narrow passages, known as 'rifts', developed by phreatic solutional enlargement of fractured rifts.

The streamway in the inner part of the system formed within the limestone is characterised by deep phreatic loops reaching depths as much as 90 metres (300 ft), with the water flowing down-dip along bedding planes and rising up enlarged joints.

[21] Eilert Ekwall gives an alternative derivation of Wookey from the Old English wocig, meaning a noose or snare for animals.

[29] The designation of the water catchment area for Wookey Hole, covering a large area of the Mendip Hills as far away as Priddy Pools, as a Site of Special Scientific Interest (SSSI) during the 1970s and 1980s was controversial because of conflicts of interest between land owners, recreational cavers and cave scientists.

The final settlement resulted in a smaller area being designated and many agricultural practices being removed from the list of proscribed "Potentially Damaging Operations".

[31][32] Archaeological investigations were undertaken from 1859 to 1874 by William Boyd Dawkins, who moved to Somerset to study classics with the vicar of Wookey.

[34] Herbert E. Balch continued the work from 1904 to 1914,[35] when he led excavations of the entrance passage (1904–1915), Witch's Kitchen (the first chamber) and Hell's Ladder (1926–1927) and the Badger Hole (1938–1954), where Roman coins from the 3rd century were discovered along with Aurignacian flint implements.

[37] The 1911 work found 4 to 7 feet (1.2–2.1 m) of stratification, mostly dating from the Iron Age and sealed into place by Romano-British artefacts.

[39] Later work led by Edgar Kingsley Tratman explored the human occupation of Rhinoceros Hole,[40] and showed that the fourth chamber of the great cave was a Romano-British cemetery.

With equipment on loan from Siebe Gorman, he and Penelope ("Mossy") Powell penetrated 52 m (170 ft) into the cave, reaching the seventh chamber, using standard diving dress.

Employing semi-closed circuit nitrogen-oxygen rebreathers, between 1957 and 1960 John Buxton and Oliver Wells went on to reach the elbow of the sump upstream from the ninth chamber at a depth of 22 m (72 ft).

A few days later Geoff Yeadon and Oliver Statham somewhat controversially reached the 23rd chamber after laying just a further 9 metres (30 ft) of line.

[58][59] Taking advantage of the tunnel driven through to Chamber 20 by the show cave management in 2015, a team began seriously to investigate the leads in that area.

[61][62] A 1000-year-old skeleton was discovered in the caves by Balch in 1912, and has also traditionally been linked to the legendary witch, although analysis indicated that they are the remains of a male aged between 25 and 35.

[63] The remains have been part of the collection of the Wells and Mendip Museum, founded by Balch, since they were excavated, though in 2004 the owner of the caves said that he wanted them to be returned to Wookey Hole.

[64] It was partly the legend of the witch that prompted TV's Most Haunted team to visit Wookey Hole Caves and Mill to explore the location in depth, searching for evidence of paranormal activity.

[72] The cave and mill were joined, after purchase, by Madame Tussauds in 1973 and operated together as a tourist attraction until there was a management team buyout in 1989.

[78] The cave was used for the filming of episodes of the BBC TV series Doctor Who: the serial Revenge of the Cybermen (1975) starring Tom Baker.

In 2005, the museum reported that a Dalek prop had gone missing from its collection, and that they had received a ransom note and a detached plunger from the "Guardians of the Planet Earth".

[84] On 1 August 2006, CNN reported that Barney, a Doberman Pinscher employed as a security dog at Wookey Hole, had destroyed parts of a valuable collection of teddy bears, including one which had belonged to Elvis Presley, which was estimated to be worth £40,000 (US$75,000).

[86] In February 2009 Cottle turned the Victorian bowling green next to the caves into a crazy golf course without first obtaining planning permission.