Wookey Hole cave was formed by the action of the River Axe on the limestone hills. Before emerging at Wookey Hole the water enters underground streams and passes through other caves such as Swildon's Hole and St Cuthbert's Swallet. After resurging, the waters of the River Axe are used in a handmade paper mill, the oldest extant in Britain, which began operations circa 1610, although a corn grinding mill operated there as early as 1086.
The cave is noted for the Witch of Wookey Hole – a roughly human shaped rock outcrop, reputedly turned to stone by a monk from Glastonbury. It is also the site of the first cave dives in Britain.
The caves, at a constant temperature of , have been used by humans for around 50,000 years. The low temperature means that the caves can be used for maturing Cheddar cheese.
In 1544 products of Roman lead working in the area were discovered. The lead mines across the Mendips have produced contamination of the water emerging from the underground caverns at Wookey Hole. The lead in the water is believed to have affected the quality of the paper produced.
Herbert E. Balch continued the work from 1904 to 1914, where he led excavations of the entrance passage (1904-15), Witch's Kitchen (Chamber 1) 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. The 1911 work found a - of stratification, mostly dating from the Iron age and sealed into place by Romano-British artifacts. Finds included a silver coin of Marcia (124BC), pottery, weapons and tools, bronze ornaments, and Roman coins from Vespasian to Valentinian II.
Later work led by Edgar Kingsley Tratman (1899-1978) OBE DSc MD FSA explored the human occupation of the Rhinocerous hole, and showed that the fourth chamber of the great cave was a Romano-British cemetery.
The cave was explored by cave divers from the Cave Diving Group of Great Britain starting in the 1930s. In 1935, two Post Office engineers, Graham Balcombe and John Arthur "Jack" Sheppard penetrated into the cave, reaching "Chamber 7" using standard diving dress. The event was the first successful cave dive in Britain.
Chamber 9 , which is also known as Cathedral Cave, was reached in 1948. In April 1949, Gordon Marriott was killed while exploring the cave. The divers discovered archaeological materials in the course of these explorations.
These early explorations used oxygen, good only for dives of up to . Experiments with early scuba gear (referred to as aqualungs at the time) were undertaken, nearly ending in tragedy. Bob Davies explored Chamber 13, in 1955 "on open circuit equipment with fins." Losing his dive line, Davies was trapped for 3 hours. Thereafter, as the nascent SCUBA technology improved, the cave divers focused their attention on closed-circuit rebreather systems.
John S. Buxton, Thompson, George, and Oliver Craig Wells (grandson of science fiction writer H. G. Wells) continued the exploration of Wookey Hole in the 1950s. In April 1957, Nitrox rebreather systems were used by Buxton and Wells in exploring beyond the point in the cave designated as "Wookey 13." According to the Cave Diving Group web site, on this trip, "Suit inflation [was] used with dry suits, a significant development." In 1960, again using the rebreather technology, Buxton, Thompson and George reached Wookey Chamber 15: one of the explorers (Buxton) penetrated a feature called "The Slot": reaching "ongoing passage at 70ft (22m) depth.
During excavations in 1954-7 at Hole Ground, just outside the entrance to the cave the foundations of a 1st century hut and iron age pottery were seen. These were covered by the foundations of Roman buildings, dating from the 1st to the late 4th century.
In 1960, a home made wetsuit was used. In January 1970 John Parker reached Chamber 20, and thereafter Chamber 22.
In the 1970s, extensive tunneling and construction work was carried out to enable members of the public to pass beyond chamber 4 into sections of the cave that had previously only been accessible to cave divers.
In 1996-1997 water samples were collected at various points throughout the caves and showed different chemical compositions. Results showed that the location of the "Unknown Junction", from where water flows to the Static Sump by a different route from the majority of the River Axe, is upstream of Sump 25.
A man from Glastonbury is betrothed to a girl from Wookey. A witch living in Wookey Hole Caves curses the romance so that it fails. The man, now a monk, seeks revenge on this witch who—having been jilted herself—frequently spoils budding relationships. The monk stalks the witch into the cave and she hides a in dark corner near one of the underground rivers. The monk blesses the water and splashes some of it at the dark parts of the cave. Catching the witch off guard, the monk splashes the water at the dark corner she is hiding in. The blessed water immediately petrifies the witch, and she remains in the cave to this day.
The current paper mill building, whose water wheel is powered by a small canal from the river, dates from around 1860 and is a Grade II-listed building. The production of handmade paper ceased in Februaury 2008 after owners agreed there was no longer a market for the products, visitors to the site are still able to make paper from cotton. Other attractions included dinosaur yard, a museum about the cave and cave diving, a theatre with circus shows, House of mirrors and Penny arcades.
The cave and mill were joined, after purchase, by Madame Tussauds in 1973 and operated together as a tourist attraction. The present owner and manager is former circus proprietor Gerry Cottle who purchased the site for around £6million.
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. This has since been referenced in the comedy of The League of Gentlemen. The cave was also used in the filming of the British series "Robin of Sherwood" (1983).
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 $75,000. The insurance company insuring the exhibition of stuffed animals had insisted on having guard dog protection.