Six miles off the coast of Deal in East Kent, England, seal pups frolic on the ever-changing, intricately-patterned sands that are exposed at low tide. Beneath the water's surface is a thriving ecosystem of blue mussels, sand eels and peeler crabs.

These are the Goodwin Sands, a 10-mile stretch of sandbank that has been recommended by the Wildlife Trusts as a future Marine Conservation Zone. In addition to providing a home for a wide variety of sea life, the Sands help bolster coastal protection against erosion.

But they may disappear. The Dover Harbour Board wants to dredge 2.5 million tons from the Goodwin Sands as part of plans to expand the port – one of Europe's busiest – and provide much-needed regeneration to Dover's seafront.

However, the board has met resistance. Some of that is due to environmental factors. But there is another reason, too: the Goodwin Sands are home to Britain's largest underwater graveyard.

Hidden just beneath the water's surface at high tide, the Sands are one of the most dangerous spots in the English Channel. During storms they can be particularly deadly.

The Goodwin Sands are home to Britain's largest underwater graveyard

In late November 1703, when southern Britain saw the worst natural disaster in its history, a massive cyclone now known as the Great Storm, more than 1,000 seamen died on the Goodwin Sands.

Among the many ships lost that night was HMS Stirling Castle, which was discovered by local divers in 1979. Since 1980, it has been a designated protected wreck under the 1973 Protection of Wrecks Act – meaning access to it is restricted in order to prevent vandalism and salvage operations.

A century later, on 24 January 1809, the East India Company ship the Admiral Gardner departed from London bound for Madras. It carried a cargo of iron, guns, anchors, and 48 tons of company coins – currency for the workers in India.

As the ship passed the coast of Kent, a fierce gale blew in. It ran aground on the Goodwin Sands along with two other East India ships that same night. Efforts to save the ship were futile, although somewhat miraculously, only one life was lost.

These three East India Company ships, as well as HMS Stirling Castle, are just a few of more than 1,000 shipwrecks buried beneath the Goodwin Sands. Some believe the number of wrecks may be as high as 2,000.

When the Sands were dredged in 1979 for construction at Dover Harbour, workers found East India Company coins in the material. A few years later, salvage operations at the Admiral Gardner recovered more than one million coins before the wreck was designated a protected area. There is now a 300m (985ft) exclusion zone around its remains.

The Goodwin Sands serve as breeding grounds for the local seal population

The Dover Harbour Board says these exclusion zones will remain untouched. The dredging process will be limited to an estimated 0.22% of the total volume of the Goodwin Sands, says the board's spokesperson Antony Greenwood. What's more, anomalies that have been identified by archaeological surveys – potentially other shipwrecks – will be left untouched.

But opponents point out that the Goodwin Sands are a closed system, meaning that the Sands are all one entity, constantly moving in a circular direction, with little material moving in or out. As a result, says Stephen Eades of the marine conservation nonprofit Marinet, "If they were to dredge this site, any hole will be filled by sand from elsewhere within the Goodwin Sands system, thereby exposing and damaging other sites."

In other words, work in one area could place the whole Sands at risk.

Greenwood disagrees, noting that larger amounts of sand were dredged from the area in the 1970s and again in the 1990s when construction of the Channel Tunnel was underway. These procedures appear to have done little to no damage to the Goodwin Sands – though it is worth noting that detailed before-and-after surveys were not carried out to measure possible changes in the marine ecosystem.

This entire area is a collective war grave – Stephen Eades

That ecosystem is another part of why campaigners are fighting against dredging. Among other things, the Goodwin Sands serve as breeding grounds for the local seal population and as a spawning site for herring and other fish.

The Sands also provide coastal protection against erosion and flooding. A natural breaker, they absorb some of the energy from the waves that pound this part of the coast. That is particularly important to the communities of Deal and Kingsdown, where flood defences are currently under construction at a cost of almost £10 million.

The best chance anti-dredging campaigners have, though, might have nothing to do with flooding, marine animals or even shipwrecks at all. "This entire area is a collective war grave," says Eades.

In 2013, the last surviving Dornier World War Two bomber was raised from the Goodwin Sands, where it had been shot down during the Battle of Britain. The German aircraft is now undergoing restoration work at RAF Cosford.

They will only see the damage or destruction once it has occurred

But a number of World War Two planes and their crews remain buried beneath the Sands. David Brocklehurst of the Kent Battle of Britain Museum has compiled a list of 60 aircraft believed to have landed or crashed on the Goodwin Sands in 1940 alone. Of these, at least 50 had crews listed as killed or missing.

Air Force historians are double-checking the accuracy of Brocklehurst's list, which could upend the plans to dredge. Under the terms set out in The Protection of Military Remains Act (1986), it is an offence to disturb a site where there is military aircraft wreckage and likely human remains.

Greenwood points to a series of procedures that will mitigate any potential damage to historic sites, like having an archaeological consultant on board the dredger to ensure correct protocols are followed. But opponents believe more needs to be done.

In a letter to the Marine Management Organisation opposing the licensing application, the Nautical Archaeology Society argues that having observers on the dredging vessels will not help, since "they will only see the damage or destruction once it has occurred."

Some believe the number of wrecks may be as high as 2,000

The period for public comment on the dredging closes in November 2016, after which the Marine Management Organisation will make a decision. Even if a license is granted, the Ministry of Defence could prohibit any activity while further research into the World War Two aircraft is conducted.

And if the permissions are granted? It is possible that the dredging will have no lasting effect on the Sands or the coastal towns of Kent.

But with a potentially risky future for local residents, the question remains about whether the dead should be left to rest in peace aboard their vessels – and the Goodwin Sands allowed to keep its mysteries.

This story is a part of BBC Britain – a series focused on exploring this extraordinary island, one story at a time. Readers outside of the UK can see every BBC Britain story by heading to the Britain homepage; you also can see our latest stories by following us on Facebook and Twitter.