This stretch of coast originally consisted of salt marshes protected from the sea by ridges of shingle and sand, and Holkham's Iron Age fort stood at the end of a sandy spit surrounded by the tidal wetland.

The Vikings navigated the creeks to establish Holkham village, but access to the former harbour was stopped by drainage and reclamation of the marshes between the coast and the shingle ridge which started in the 17th century, and was completed in 1859.

The NNR has taken steps to control entry to the fragile dunes and other areas important for their animals or plants because of the damage to sensitive habitats that could be caused by unrestricted access.

To the east of the Wells Channel, the reserve is mainly salt marshes and mud flats, and is difficult and potentially dangerous to access, although a public footpath runs along the southern edge of these tidal areas.

[5][6] The salt marshes on this coast are stated in the Site of Special Scientific Interest (SSSI) notification document to be "among the best in Europe ... the flora is exceptionally diverse".

[14] Until the 17th century, ships could navigate the tidal creeks to reach the staithe (harbour) at Holkham village, but local landowners began to reclaim the marshes from 1639, and the final embankment at Wells was constructed by the 2nd Earl in 1859, completing the conversion of about 800 hectares (2,000 acres) to farmland.

The 3rd Earl planted Corsican, maritime and Scots pines on the dunes in the late 19th century to shelter the agricultural land from wind-blown sand,[5][12] which is carried inland when the wind speed exceeds three metres (10 ft) per second and blows from directions between northwest to northeast.

[17] The shingle banks and foreshore hold wintering flocks of shore larks, snow buntings and twite,[7] and waders like knots, curlews, dunlins and grey plover probe for invertebrates in the mud flats.

[17] Holkham's north-facing coastal location can attract large numbers of migrating birds in autumn if the weather conditions are right,[20][21] especially with north to north-east wind.

[25] Grayling, small heath and common blue butterflies can be found in the dunes,[26] where there is also a large antlion colony, making Holkham one of only two locations for this predatory insect in the UK.

[25] On exposed parts of the coast, the mud and sands are scoured by the tides, and have no vegetation except possibly algae or eelgrass, but where the shoreline is more protected, internationally important salt marshes can form, with several uncommon species.

[7] Scrubby sea-blite and matted sea lavender are characteristic plants of the drier upper salt marsh here, although they are uncommon in the UK away from the Norfolk coast.

[29] The discovery of the nationally rare tiny earthstar fungus at Holkham led its finders to state that "The survival of this species in Britain would undoubtedly benefit from the construction of a boardwalk across this fragile and frequently-visited habitat.

"[30] The Little Tern colony at Holkham, holding seven per cent of the British population, is cordoned off in the breeding season, with signs explaining why people are excluded from the area.

[36] Unlike the soft, rapidly eroding cliffs further east,[37] the coast of the SSSI has shown a less consistent pattern, with a net accretion of beach material between 1880 and 1950.

[40] The Environment Agency's management plan until 2105 is to rely on the natural protection of the dunes, intervening only if work is necessary to maintain their effectiveness in the face of a potential sea level rise of 1.1 m (3 ft) by that date.

This may affect the movement of sediment, and lead to some erosion of the dunes and beaches at Holkham, but should not destroy their effectiveness as a sea defence unless the island reattaches to the mainland at some date in the distant future.