A dolerite dyke of Ordovician age can be seen in the melange at Trwyn y Gorlech in the north. There is an olivine dolerite dyke of Tertiary age at Cafn Enlli in the southeast. Further dykes can be seen in the cliffs at Ogof y Gaseg and at Ogof Hir.
A thin spread of glacial till stretches across the centre of the island. This was left behind by the Devensian Irish Sea Icesheet. There is a small patch of blown sand at Porth Solfach on the west coast and a landslip at Briw Cerrig at the foot of the cliffs on the east coast.
People lived on the island in Neolithic times, and traces of their hut circles remain. During the 5th century the island became a place of refuge for Christians and a small Celtic monastery existed. In 516 Saint Cadfan arrived from Brittany and directed the building of St Mary's Abbey. In medieval times three pilgrimages to Bardsey Island were said to be equal to one visit to Rome. In 1188 the abbey was still a Celtic institution, but by 1212 it belonged to the Augustinians. Many people still walk to Aberdaron and Uwchmynydd each year in the footsteps of the saints. Only ruins of the old abbey's 13th-century bell tower remain. A Celtic cross in the ruins commemorates the 20,000 saints claimed to be buried on the island.
Saint Deiniol, the bishop of Bangor, was buried on the island in 584. Saint Dyfrig was also buried on Bardsey Island, although in 1120 his remains were moved to Llandaff.
The "Dissolution of the Lesser Monasteries Act" of 1536, on the orders of Henry VIII, resulted in "St Mary's Abbey" being closed and its buildings pulled down in 1537. The choir stalls, two screens and the bells were moved to Llanengan, where the parish church was then being built.
For many years Bardsey Island formed part of the Newborough Estate. Between 1870 and 1875 the island's farms were rebuilt. A small limestone quarry was opened, and a lime kiln set up. "Carreg" and "Plas Bach" are separate buildings, but the remaining eight were built as semi-detached houses, each pair with outbuildings set around a shared yard. The buildings are Grade II listed. In 2008, Cadw gave £15,000 to help with some repairs. Only one of the original "croglofft" cottages, "Carreg Bach", is still standing. Given the choice of a harbour or a new church, in 1875 the islanders asked for a place of worship; a Methodist chapel was built.
The island had a population of 132 in 1881; by 1961 it had fallen to 17. The island's small school, opened in a former chapel in 1919, closed in 1953. By 2003 the population was down to 4.
"Bardsey Island Trust ()" bought the island in 1979. It was given money by the Church in Wales and many Welsh academics and public figures. The trust gets its money from membership subscriptions, grants and donations. It wants to protect the wildlife, buildings and archaeological sites of the island. It also promotes its artistic and cultural life, and wants people to visit as a place of natural beauty and pilgrimage. In 2000, the trust advertised for someone to run the sheep farm on the island. They had 1,100 applications. The farm is now run by the "Royal Society for the Protection of Birds"; and the land is managed to keep the natural habitat. Oats, turnips and swedes are grown; goats, ducks, geese and chickens kept; and there is a mixed flock of sheep and Welsh black cattle.
An old and twisted apple tree was found growing by the side of "Plas Bach." It is believed to be all that is left of an orchard planted by the monks who lived there a thousand years ago. In 1998, experts on British apples said this tree was the only example of the "Bardsey Apple ()". The tree has been propagated by grafting and is available commercially.
Bardsey Lighthouse stands on the south end of the island and guides vessels passing through St George's Channel and the Irish Sea. It is the only square lighthouse looked after by Trinity House.
Lt. Thomas Evans R.N., asked for a light on the island in 1816. In 1821 Trinity House built the lighthouse at a cost of £5,470 12s 6d with another £2,950 16s 7d for the lantern.
Joseph Nelson was the engineer and builder. He had served under Daniel Alexander, a Trinity House architect, whose influence can be seen on parts of the design including the heavy weathered string-course near the base and the blocked and hooded directional-light window. Joseph Nelson is linked to the design of at least 15 lighthouses, mostly in the Bristol Channel.
The Lighthouse is built of ashlar limestone and is not plastered. It is painted in red and white bands on the outside. The Lighthouse tower is 30 m (98 ft) high and is unusual because it is square, not round. Unlike many other lighthouses, it has kept its original gallery railings, which are of iron and bellied (i.e. curved out in width at their crowns) towards the top. The present lantern, fitted in 1856, did not need the original railings to be taken down.
The walls are 1.2 m (4 ft) thick at the base and 0.9 m (3 ft) at the top.
At first, the light had reflectors but changed to a dioptric (refracting) mechanism in 1838. The present lantern of 1856 is a 4.27 m (14 ft) wide chamfered octagon and the light is fixed, instead of revolving. The present revolving apparatus was put in place in 1873. It gives a group of five flashes, at first with an oil-lamp, but changed to electric in 1973.
The Lighthouse is unusual in lacking any sort of harbour. As it is on an established migratory route, the tower has many bird casualties. The Royal Society for the Protection of Birds, and Trinity House have tried to help the problem by providing perches on the lantern top and flood-lighting the tower, but this does not seem to have helped.
In 1987 the Lighthouse was changed to automatic operation, and is now checked by the Trinity House Depot at Harwich. A local person does regular maintenance.
"Y Storws", also known as "The Boathouse", was built a few years before the lighthouse, near the landing place at "Y Cafn".
The island was made a "National Nature Reserve" in 1986, and is part of "Glannau Aberdaron ac Ynys Enlli Special Protection Area ()". It is now a favourite bird-watching location, on the migration routes of thousands of birds. "Bardsey Bird and Field Observatory" (), founded in 1953, nets and rings 8,000 birds each year to study their migration patterns.
The island was made a Site of Special Scientific Interest because of its maritime life. This includes internationally rare lichens; bryophyte, plants, bird species; and intertidal communities. Nationally important flowering plants include sharp rush, rock sea lavender, small adder's tongue, western clover, and the rare purple loosestrife. Two nationally rare heathland lichens are found on the slopes of "Mynydd Enlli": the ciliate strap lichen and golden hair lichen; and there are over 350 lichen species in total. The leafcutter bee, which cuts neat, rounded circles in rose leaves, used to seal the entrance to its nest, is native.
Thousands of birds pass through each year on their way to their breeding or wintering grounds. Chiffchaffs, goldcrests and wheatears are usually the first to pass through, followed by sedge warblers and willow warblers, whitethroats and spotted flycatchers.
About 30 species of bird regularly nest on the island, including ravens, little owls, oystercatchers and the rare chough. Hundreds of sea birds, including razorbills, guillemots, fulmars and kittiwakes, spend the summer nesting on the island's eastern cliffs. There are no land predators such as rats or foxes on the island. On a dark moonless night an eerie cackling can be heard across the island as 7,000 pairs of Manx shearwaters, 3.5 per cent of the British population, come ashore to lay and incubate their eggs in abandoned rabbit warrens or newly dug burrows.