The reserve is important for some scarce breeding species, such as pied avocets on the islands, and western marsh harriers, Eurasian bitterns and bearded reedlings in the reeds, and is also a major migration stopoff and wintering site.

Despite centuries of embankment to reclaim land and protect the village, the marshes have been flooded many times, and the southward march of the coastal shingle bank and encroachment by the sea make it inevitable that the reserve will eventually be lost.

Both Modern and Neanderthal people were present in the area before the last glaciation between 100,000 and 10,000 years ago, and humans returned as the ice retreated northwards.

[6] John Heydon started the process of embanking the marshes to reclaim the land in 1522, and his banks were extended and improved by Dutchman Jan van Hasedunch from 1630.

[8] Further enclosure in the mid-1820s aggravated the problem, and also allowed the shingle ridge at the beach to block the former tidal channel to the Salthouse marshes to the east of Cley.

[9] In an attempt to halt the decline, Thomas Telford was consulted in 1822, but his recommendations for reducing the silting were not implemented, and by 1840 almost all of Cley's trade had been lost to Blakeney and other Norfolk ports.

[9] In the mid-nineteenth century, the Lord of the Manor constructed the present road to the beach in exchange for closing the ancient right of way across the marshes.

[6] In the decades preceding World War I, this stretch of coast became famous for its wildfowling; locals were looking for food, but some "Gentleman Gunners" hunted to collect rare birds.

[11][12] The reserve was extended in 1962 through the lease of the adjacent 11-hectare (27-acre) Arnold's Marsh from the National Trust;[13] this had long been the primary feeding area for waders, but much of the best habitat had been lost to the advancing shingle ridge.

During the Second World War, Royal Artillery military fortifications were established at the beach end of the reserve, including two 6-inch (15.24 cm) guns, five buildings, two pillboxes, a minefield,[3] and concrete anti-tank blocks.

[26] The success of the centre has led to plans to develop it further, offering more services and educational facilities and enhancing its profitability for the Trust.

This purchase would create a unified 8 km (5 mi) stretch of NWT-owned coastal land and expand the Cley reserve by one-third.

[28][29] The key breeding species are reed bed specialists such as the marsh harrier, Eurasian bittern and bearded reedling, and the island-nesting avocet.

Some, such as Eurasian whimbrels, curlew sandpipers and little stints, just pausing for a few days to refuel before continuing south, others staying for the winter.

[32] Barn owls and sometimes hen harriers quarter the marshes in winter, and snow bunting flocks can be found on the beach.

[39] In order to maintain a good habitat, parts of the reed bed are cut and sold for thatch each year to establish a mosaic of plants of different ages.

[40][41] Brown hares are widespread, and European otters may be seen, with spraints regularly found at the southern end of East Bank.

The upper saltmarsh has a number of scarce species including lesser centaury, curved hard-grass and sea pearlwort, with soft hornwort in the dykes.

The site is generally rich in plants, especially those that can cope with saline environments, but three species appear to have been lost: divided sedge was last recorded in 1999, grey hair-grass in 1982 and lax-flowered sea lavender in 1977.

The locally rare bryophyte Heim's pottia occurs in the saltmarsh, and the coastal variety piliferum of cuspidate earth-moss is found at Salthouse.

[42] A 2005 survey at Cley and five other North Norfolk coastal sites found that 39 per cent of visitors gave birdwatching as the main purpose of their visit.

[48] The large number of tourists can have negative effects; wildlife may be disturbed, particularly species that breed in exposed areas, such as ringed plovers, and plants can be trampled, which is a particular problem in sensitive habitats such as sand dunes and vegetated shingle.

[50] The access paths to the hides, other than the northernmost, are largely boardwalked,[30] and an extensive programme of fence replacement and improvements to the control of water levels on the reserve took place in 2010–2011.

[31] The reserve shelters behind a ridge of shingle that runs west from Weybourne along the Norfolk coast, before becoming a spit extending into the sea at Blakeney Point.

[4] The landward movement of the shingle also means that the channel of the River Glaven becomes blocked increasingly often, leading to flooding of the reserve and Cley village.

[55] The Environment Agency considered a number of remedial options to protect these vulnerable areas,[54] and a new route for the river to the south of its original line was completed in 2007 at a cost of about £1.5 million.