The island has an area of 2.92 km2 (1.13 sq mi). Its highest point is 79 m (259 ft) above sea level at Gorse Hill, while the majority of the island sits at around 60 m (200 ft) above sea level. Skomer is intersected by a series of slopes and ridges giving it a rich and varied topography. It is approximately 2.4 km (1.5 mi) from north–south and 3.2 km (2.0 mi) east–west. The island is almost cut in two near its eastern side by two bays. It is one of several islands lying within a kilometre of the Pembrokeshire coast and separated from the mainland by the treacherous waters of Jack Sound. Three islets surround Skomer: Mew Stone (60 metres, 197 feet), Midland Isle, (50 metres, 164 feet), and Garland Stone, (32 metres, 105 feet).
The volcanic rocks of which Skomer is comprised date from the Silurian period around 440 million years ago. A series of basalts, rhyolites, felsites, keratophyres, mugearite and associated sedimentary rocks (quartzites, etc.) are grouped together as the 'Skomer Volcanic Series'. The series which is up to 1000m thick also includes trachyte, dolerite and skomerite which is an altered andesite. Basalt is the most common component of this sequence; some of it appears as pillow lava indicating that it was erupted under water. Other basalt flows show signs of contemporary sub-aerial weathering.
This same suite of rocks can also be traced eastwards on the mainland along the northern side of the Marloes peninsula and extends almost as far east as St Ishmael's. The entire sequence on Skomer dips between 15° and 25° to the south-southeast. It is cut by several faults, notably those responsible for the erosion of the inlets of North Haven and South Haven. A NW-SE aligned fault stretches between Bull Hole and South Haven, offsetting the strata on either side.
Skomer was cut off from the mainland by rising sea levels after the last Ice Age.
There is evidence of human occupation—field boundaries and settlement remains—dating back to the Iron Age. The Skomer Island Project, run jointly by the Royal Commission for Ancient and Historical Monuments in Wales (RCAHMW) with archaeologists from the University of Sheffield and Cardiff University, started in 2011, investigates the island's prehistoric communities. Airborne laser scanning together with ground excavations continued in 2016 and established that human settlement dates back 5,000 years. Rabbits were introduced in the 14th century and their burrows and grazing have had a profound effect on the island landscape.
It was last permanently inhabited by the Codd family (all year round) in 1950. After the Second World War, the owner had offered the West Wales Field Society, now The Wildlife Trust of South and West Wales, the opportunity to make a survey of Skomer which was accepted and Skomer opened for visitors from April 1946. The farm buildings in the centre of the island, now housing visitor accommodation, were refurbished in 2005. Skomer was featured in the BBC TV documentary Coast in Episode 4 of Series 5 (first aired August 2010).
David Saunders MBE was in 1960 the first warden of Skomer.
Skomer is best known for its large breeding seabird population, including Manx shearwaters, guillemots, razorbills, great cormorants, black-legged kittiwakes, Atlantic puffins, European storm-petrels, common shags, Eurasian oystercatchers and gulls, as well as birds of prey including short-eared owls, common kestrels and peregrine falcons. The island is also home to grey seals, common toads, slow-worms, a breeding population of glow-worms and a variety of wildflowers. Harbour porpoises occur in the surrounding waters. The Skomer vole, a sub-species of bank vole, is endemic to the island.
There are around 10,000 breeding pairs of puffins on Skomer and Skokholm Islands, making them one of the most important puffin colonies in Britain. They arrive in mid-April to nest in burrows, many of which have been dug by the island's large rabbit population. The last puffins leave the island by the second or third week in July. They feed mainly on small fish and sand eels; often puffins can be seen with up to a dozen small eels in their beaks. After a period of declining numbers between the 1950s and 1970s, the size of the colony is growing again at 1–2% a year (as of 2006). By 2004, there were numerous puffin burrows on the island and adults flying back with food run across the walkways oblivious to the tourists.
An estimated 310,000 pairs of Manx shearwater breed on Skomer, with around 40,000 pairs on the "sister" island Skokholm. These colonies jointly comprise around half the world population and make the islands the world's most important breeding site for the species. The birds usually nest in rabbit burrows, a pair reportedly using the same burrow year after year.
Shearwaters are not easy to see as they come and go at dusk, but a closed-circuit television camera in one of the burrows allows subterranean nesting activity to be seen on the screen in Lockley Lodge on the mainland at Martin's Haven. The remains of shearwaters killed by the island's population of great black-backed gulls can also be seen. An overnight stay in the hostel run by the Wildlife Trust of South and West Wales allows guests to hear and see the shearwaters.
The Manx shearwater has a remarkable life. After fledging the young birds migrate to the South Atlantic off the coasts of Brazil and Argentina. They remain there at sea for five years before returning to breed on their natal island. On their return they navigate back to within a few metres of the burrow in which they were born. As they are ungainly and vulnerable on the land, they leave their burrows at dawn for the fishing grounds some fifty kilometres north out in the Irish Sea, not returning until dusk. Thus they attempt to avoid the gulls to which they would fall easy prey.
Skomer has one unique mammal: the Skomer vole (Myodes glareolus skomerensis), a distinct form of the bank vole. The lack of land-based predators on the island means that the bracken habitat is an ideal place for the vole, with the population reaching around 20,000 during the summer months. Then the resident short-eared owls may be seen patrolling the areas close to the farmhouse in the centre of the island for voles to feed their young.
Boats sail to Skomer from Martin's Haven on the mainland, a sheltered 10-minute trip every day except Monday (Bank Holiday Mondays excepted) from April to October between 10am and noon (actual times may vary). Return sailings are from 3pm but the boatman will advise on the day. There are limits on the number of people allowed to visit the island (250 per day). Advance booking is not permitted and reservations are strictly on a first come, first served basis at Lockley Lodge in Martin's Haven and long queues can develop early each morning.
Areas open for visitor access are restricted to pathways. The Neck, an eastern area connected only by a narrow isthmus, is entirely out of bounds to visitors.
In 2005–06, there was a renovation project of the farm buildings which included the old barn for improved overnight visitor and research accommodation, the volunteers' quarters were rebuilt and the warden's house at North Haven was also rebuilt. Solar power provides hot water and electricity for lighting. Self-catering visitor accommodation is now available from April to October.