After 12 weeks of digging in the rain, the huge expanse of land at the corner of St Michael's Hill and Tyndall Avenue, looks like a quagmire.

At first sight, the enormous expanse of red mud and claggy puddles doesn't give the impression that it could tell you much about Bristol's past, but archaeologist Andy King is clearly excited about what his team from the Bristol and Region Archaeological Service (BARAS) has learnt over the last three months.

"We've basically rewritten the history of Bristol with this dig," he says, as he looks out across the site from beneath the peak of his hard hat.

"For years people have written about the Royal Fort that once stood here, without ever really knowing much about it.

"Now, for the first time, we've been able to properly dig down and find concrete evidence of the structure."

The Royal Fort, designed by Sir Bernard de Gomme, one of the greatest military engineers of his time, was planned not only to defend Bristol, but also to serve as the western headquarters for the Royalist Army, under Prince Rupert.

It was built over a smaller Parliamentary fortification, known as the Windmill Hill Fort, after Prince Rupert had been installed as governor of Bristol in August 1643, following the capture of the city by the Royalist Army.

"When we say fort, you shouldn't think of a big castle," Andy says. "The fort was basically an enormous earthwork – a mound with bastions, which would act as a defensive headquarters for the Royalist army, and provide commanding views across the city.

"From up here you would have been able to see far into Somerset and up to Gloucester – if a Parliamentarian army was heading towards the city, you would know about it in plenty of time."

The Fort remained in Royalist hands until September 1645, when it was surrendered, along with the city, to Oliver Cromwell and his New Model Army.

The Parliamentary army may have added to the defences, but these were demolished on Cromwell's orders in 1655-6.

A magnificent mansion – Royal Fort House – was built on the site in 1761 for Thomas Tyndall.

It was occupied by the Tyndall family until 1916 when it came into the possession of the then recently-founded University of Bristol, along with the surrounding land.

The H. H. Wills Physical Laboratory was built opposite in the mid-1920s and the University has continued to grow around Royal Fort ever since.

The recent demolition of 1950s physics workshops and 1930s nursing accommodation, has given the archaeologists the opportunity to dig on the site for the first time in generations.

A new £90-million bioscience block is planned for the land – including part of the old Children's Hospital site on the corner of St Michael's Hill and Tyndall Avenue.

The development will consist of a striking new building housing research and teaching facilities for the School of Biological Sciences, as well as a new route into Royal Fort Garden from St Michael's Hill.

"That's why we were employed by the university to get in here to find out what we could while we still had the opportunity," Andy says.

"In actual fact, when the Parliamentarians did come into the city, they approached via Old Market – which was then the weakest part of the Royalist fortifications.

"So the fort was never the scene of a battle. If it had been, we could have expected to find all kinds of evidence – including mass graves. But we knew that hadn't happened, so we thought we might not find much here at all.

"Early on we found part of the defensive moat, which would have surrounded the fort. But we've found no evidence of a wall around the structure – which seems to have made its way into the history books via the imagination of Victorian historians." But the most exciting finds for the 11-strong team of archaeologists have been the remains of a pair of buildings, which would once have stood inside the fort.

"One, we believe, would have been the barracks for the 150-odd men that would have been stationed here by the Royalists. You can clearly see the outline of the walls, the doors, and even where a staircase might have been. Inside the building we found a cache of 33 unfired musket balls."

But the most exciting find came at the other side of the site.

"We discovered an enormous structure – a room that had been carefully dug down deep into the bedrock and lined with stone.

"There is much debate over what this building was – but I am convinced that it must have been the magazine, where the Royalists kept their gunpowder – their most valuable possession during those days of civil war.

"I'm sure there will be years of academic debate over whether it really is the fort's magazine, but I'm pretty much convinced until somebody can come up with a better idea."

The dig also unearthed cannon balls, 17th century leather shoes, and a later Georgian ice house, which would have been built for the Tyndall family in the late 1700s.

"It's been a fabulous dig to work on," Andy says. "You really do feel you are touching Bristol's history – literally unearthing what happened here in the city during the English Civil War."