The clutch of homes that stood on stilts in the wetland fens of East Anglia were the envy of the local peasantry 3,000 years ago. But amid the remains of the grand wooden huts and the belongings of the well-to-do residents lurked evidence that all was not well at Must Farm, Britain’s premier bronze age settlement.

Firm, sausage-shaped lumps found skulking in the mud that swallowed the settlement after a catastrophic fire have been identified as pieces of faeces. Inside these deposits researchers found a grim array of tiny eggs – the calling card for parasitic worm infestations.

In the sanitising jargon of archaeology, the human coprolites were found to be brimming with eggs from fish tapeworms, giant kidney worms, whipworms and other undesirable creatures, pointing to a downside of the settlers’ fresh and convenient marsh diet.

“They must have been eating raw or undercooked fish, frogs or shellfish,” said Piers Mitchell, the director of the ancient parasites laboratory at Cambridge University, who studied the precious deposits. “Some might not have had symptoms but others would have known about it.”

Once fish tapeworms have set up home in the gut they can grow to a length of 10 metres, coiling around the twists and turns of the intestines. The most infested inhabitants in the Must Farm community probably would have been anaemic as the worms absorbed food intended for their hosts.

Prehistoric parasite eggs of a fish tapeworm (left) and a giant kidney worm (right). The samples came from the 9th-century BC Must Farm. (Black scale bar represents 20 micrometres). Photograph: M Ledger/SWNS

Kidney worms are more reasonable in size but properly fed will still reach a metre and destroy the organ in the process. Other parasites called Echinostoma worms are only 1cm long when fully grown, but heavy infestations inflame the intestines, causing abdominal pain, diarrhoea, weight loss and tiredness.

The remains of the settlement were first uncovered in 1999 during digs at a brick clay quarry at Must Farm, which is on the outskirts of Peterborough. Since then, excavations have revealed the full extent of the site. Built on stilts over a tributary of the River Nene, the settlement had five wooden huts with wicker floors and clay chimneys. The huts were connected by timber causeways and protected on the land side by a long wooden palisade.

The site dates to 900BC and was not a long lived community. Through accident or attack the settlement was engulfed in flames, perhaps only months after it was built, leaving the homes and their contents to plunge into the water. Today, these homes are the most completely preserved prehistoric domestic structures in Britain.

Among the burnt timbers of what has been described as a fenland Pompeii, archaeologists have found glass and amber beads imported from the continent, delicately woven linen, weapons, kitchen tools, pottery and the largest bronze age wheel ever found in the UK.

Probable construction of the Must Farm stilt houses. Photograph: V Herring/SWNS

And then there are the coprolites. Writing in the journal Parasitology, the researchers explain how they hand-fished 15 prehistoric poos from the waterlogged mud. Chemical analyses found that four belonged to people and seven to dogs, with the remainder of uncertain origin. Peering at pieces under the microscope, the researchers confirmed a variety of parasites from the eggs, which measure only a fraction of a millimetre long. Some pieces had more than 10,000 eggs per gram.

Whipworm eggs found in the faeces could have come from slaughtered pigs, but many of the other parasites are spread by people eating raw fish, amphibians and molluscs, the researchers said.

“This is really interesting for us. It’s one of the very few chances we’ve had to look for evidence of parasitic infection in the bronze age,” said Marissa Ledger, a biological anthropologist on the Cambridge team. “It’s possible that a lot of these eggs were passing through the system, but a lot of people would have been infected. In a single coprolite we’re finding eggs from multiple different species.”

The haul includes the earliest evidence of fish tapeworms, Echinostoma worms, Capillaria worms and giant kidney worms in Britain.

By living over the water, the Must Farm residents were somewhat protected from common parasites such as roundworms, which are spread by direct faecal contamination of food. But the location left them vulnerable to other infections.

Thick reed beds and stagnant water beneath the huts made sure that excrement dumped in the marsh did not travel far; instead it provided fertile ground in which the parasites could thrive and infect the local wildlife. That wildlife, eaten raw or undercooked, acted as the disease vector spreading the worms to the human residents and their pets.

The Must Farm work should help scientists understand the conditions that can drive human infections. “A lot of the parasites we found still affect people today, not necessarily in Britain but in other parts of the world,” Ledger said. “If we can understand the environments that help them flourish, we can use that to combat these diseases.”