A dozen white, plastic fish boxes stand jumbled on the floor of a former fish-gutting plant in the pretty town of Urk in the northern Netherlands. Each box overflows with what appear to be large, serrated pebbles or small serrated boulders. In fact, they are the fossilised teeth of mammoths. Some are as big as melons. Others are the size of cricket balls – the molars of baby mammoths, which died prematurely from hunger, or the claws and fangs of a predator, 40,000 years ago.

All around is a prehistoric boneyard. Propped against the walls are immense, curved mammoth tusks or mammoth thigh bones, five feet high. On the shelves are fragments of the jaw bone of a woolly rhinoceros and the skull and horns of a 10,000-year-old, extinct species of giant bison.

All have been scooped accidentally from the bed of the North Sea by Dutch beam trawlers in the last few months. Most are destined to be sold on to specialist sites on the internet.

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They are just a fragment of an immense North Sea bone harvest – a "by-catch" of fossils. In the past 18 years, powerful Dutch beam trawlers and dredgers are estimated to have landed 200 tonnes of the fossilised remains of animals from a score of different species (and the remains and artefacts from human beings of two different species). In the past 40 years, it is estimated, Dutch trawlers have landed 15,000 mammoth teeth alone. This, in turn, is probably only a minuscule fraction of a treasure-trove of prehistory which lies still undiscovered under the grey waves between the coasts of England and the Netherlands.

The fact that the lower North Sea was once (until about 7,500 years ago) a land bridge between Britain and the continent is well enough known. What has only recently and gradually become accepted – by scientists who for many years ignored the evidence on their own watery doorsteps – is that the area now covered by the North Sea was not just a barren "land bridge". It was for tens of thousands of years a teeming plain of Ice Age wildlife, equivalent to the richest game reserves of Africa.

Dick Mol, a Dutch customs official and amateur palaeontologist who has become one of the greatest living experts on the "lost world" of the North Sea, calls it "a Serengeti with its coat on". The man who runs the fossil clearing station at Urk is Albert Hoekman, 44, a former fisherman who now works part-time as a collector and wholesaler of bones to the world fossil trade. Mr Hoekman is a key member of a network set up by Mr Mol and his friends. He visits fishing boats when they arrive in ports all over the Netherlands each Thursday and Friday morning and buys their by-catch of bones. He tries to ensure that historically or scientifically interesting fossils are set aside for examination by experts. The rest go for sale on the internet or directly to museums or collectors.

It is to this informal system that the scientific world owes many important North Sea discoveries. "I was a fisherman myself for 17 years," Mr Hoekman said. "There was a time not long ago when we fished up this stuff and we just threw it back in the sea. We had no idea what it was. OK, it was obviously something much larger than a drowned cow but that didn't interest us much."

The remains of mammoths, of three different species of woolly rhinos as well as hippos, lions, bears, wild horses, bison, elk, reindeer, hyenas, wolves and sabre tooth cats of at least two species have been trawled from the bottom of the North Sea in the past 140 years (but with increasing intensity in the past 20 years as bottom-scraping, beam trawlers have become more powerful).

A fossil leg bone brought up from the sea bottom by a Dutch beam trawler last year proved that a giant sabre-toothed cat, as heavy as a horse, lived on the "North Sea plain" around a million years ago – much further north than scientists had previously imagined.

The discovery of part of a Neanderthal skull by a Dutch shell dredger in 2001 – first publicised last month – suggested that our enigmatic, hirsute near-cousins were active on what is now the bed of the North Sea 60,000 years ago. Scores of artefact finds by Dutch boats suggest that the mysterious Mesolithic people, who lived between the two stone ages, had widespread settlements in the very middle of what is now the North Sea around 10,000 years ago.

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This landscape – or the final version of a series of appearing and disappearing landscapes spread over more than 1.5 million years – was finally obliterated by global warming and the gradual melting of the last great ice sheet about 7,500 years ago.

A team of palaeontologists from Birmingham University – Vincent Gaffney, Simon Fitch and David Smith – has mapped a part of this vanished world, by computerising seismic survey data from the oil industry. In a book published last year, Europe's Lost World; the Rediscovery of Doggerland, they electronically pulled away the shrouds of sea-water and mud to trace the river valleys, giant lakes and the low hills of a "paradise lost" as large as the United Kingdom.

The Doggerland book is evidence of a growing scientific interest in the lost land below the North Sea. The interest has been awakened partly by the sheer volume, and the scientific importance, of fossil discoveries by trawlers in recent years but also by fears that man-made global warming could produce a renewed melting of the ice cap.

Stories of lost lands below the sea – from the Greek "Atlantis" to the Irish "Tir na n'Og" (land of eternal youth) – are part of human legend. Climate change, and the threat of the flooding of low-lying land, could also make them part of our future.

The renewed scientific interest has also brought accusations that the bed of the North Sea is being pillaged and that potentially important discoveries are being lost to science. Dutch trawlers, it is suggested by some archaeologists in Britain and France, are turning away from the unprofitable business of fishing for fish and have taken to fishing for bones. On the internet, the archaeologists point out, there are several US-based, fossil trading sites which are fed almost exclusively by trawler finds from the North Sea.

All of this amuses, and slightly angers, the team of self-taught, but expert Dutch palaeontologists, including Dick Mol, who have been trying for years to persuade the international, scientific community that the bed of the North Sea is a remarkable place. Far from being criticised, they say, the Dutch trawling industry should be praised for discovering, and for rescuing, so much. Are Dutch beam trawlers really going out looking for fossils to adorn New York or Los Angeles living rooms? "This is total bullshit," said Mr Mol. "It could not possibly be commercially viable for trawlers to do this."

Eighteen years ago, Mr Mol and a group of friends began to organise the Dutch fishing industry into a network of "accidental archaeologists". They gave the skippers of beam trawlers cash incentives to keep all the fossils that they found, however dull or ugly, and to keep detailed logs of where they found them.

Klaas Post, a fishing industry executive from Urk, is another member of Mr Mol's team. (It was Mr Post who was responsible for the first sabre-toothed cat find in 2000.) "It is ridiculous to say that Dutch trawlers are deliberately fishing for bones to sell," he said. "They would never find enough fossils to pay for their ship's fuel. There is, of course, a demand for North Sea fossils from collectors but it is not a limitless market. There are more than enough fossils coming from normal fishing to provide what the collectors want."

The only Dutch bone-fishing expeditions – 16 of them in the past eight years – have been organised for scientific purposes and paid for by Mr Mol, Mr Post and their friends or by documentary film companies. Since joining up with Mr Mol and Mr Post and their team, the former fisherman, Mr Hoekman has, himself, become a self-taught expert on Ice Age fossils. There is no real conflict between commerce and science, he says. The "phew-look-at-that" stuff that is in demand by fossil collectors – a mammoth tusk at €500 (£430) or a mammoth tooth at €60 – is usually of limited scientific interest.

Mr Hoekman admits that the system is not perfect. He hands on anything that is scientifically valuable – for instance, any bone with signs of human axe marks – to Mr Post and Mr Mol. But there are three or four other bone traders operating in Dutch fishing ports. Their interests are purely commercial. "There was one time when I saw a human skull on top of a pile of other fossils. Before I could do so, one of the other traders had bought it. We will now probably never know what it was."

British palaeontologists, including the authors of the Doggerland book, also complain that beam trawling is ravaging the bottom of the North Sea and making future scientific study of this Lost Word impossible. (Beam trawling involves dragging a heavy bar of metal along the sea floor to force flat fish, like sole, into the nets above).

"These complaints are based on ignorance of what the lower North Sea is like," said Mr Post. "There are so many currents down there and the sea is so shallow that every big storm churns up the mud on the sea bottom. This explains why we keep finding so many fossils. New ones are being forced up through the mud to the sea floor by storms all the time."

Nonetheless, beam trawling is due to be banned by the European Union in the next three or four years because, it is claimed, it damages the marine environment and uses up too much fuel. A form of "electronic" trawling", using a virtual "beam" to scare plaice and sole into the nets, is being developed.

What will this mean for the North Sea bone, or giant fossil, harvest? "No more bones. It is all coming to an end. That means no more fossil trade but also no more scientifically important finds. A pity," Mr Post, said shrugging his shoulders.

Mr Mol is not ready to give up just yet. "I am hoping that the Dutch government will keep a couple of beam trawlers for scientific or archaeological purposes," he said. "If not, I am looking into the possibility of buying one myself. How many fossils are there still down there? I would say millions."