The remains of a historic fortress, which protected the city during the English Civil War, have been unearthed at Bristol University.

The Royal Fort, which stood on St Michael's Hill, was one of the most significant fortifications of the war, which began in 1642, and was the strongest part of Bristol's defences.

Because much of the fort was destroyed in 17th and 18th centuries and its exact location, until now, had been a mystery.

In 2001, the university carried out excavations but failed to find the fort's five main bastions.

Now, after an eight-week dig by Bristol Museum and Art Gallery archaeologists, a defence ditch, two bastions and possibly the foundations of a fortification wall have been found at the summit of St Michael's Hill.

The site, which covers an area the size of two tennis courts, also revealed parts of what appear to be a 17th-century building – possibly a Civil War-period barracks block or powder store – along with artifacts including a cannonball, lead cap from a gunpowder pouch and several clay tobacco pipes.

Bruce Williams, manager of Bristol and Region Archaeological Services, directed the project.

He said: "Bristol played a prominent role in the English Civil War although the legacy of this is not so apparent within the modern cityscape.

"In addition to the remains of the Royal Fort, it is delightful to find distinguishing objects such as cannonballs that can without doubt be attributed to the Civil War period."

Mark Horton, archaeology professor at Bristol University, who conducted the 2001 excavations, said: "This is a thrilling find and allows us finally to pin down the exact spot for the fort.

"Archaeologists of the English Civil War will have to take notice of the Royal Fort, one of the very few purpose-built fortresses constructed, rather than reusing medieval castles and the like."

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

The Fort 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.

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.

According to Cromwell, it then had victuals for 150 men for 320 days. Cromwell ordered the demolished in 1655-6.

Although a number of 'gentry' houses were built on the site in the second half of the 17th century, Royal Fort House was later built, in 1761, for Thomas Tyndall and occupied by the Tyndall family until 1916 when it came into the possession of the then recently-founded University of Bristol. This year work starts on a new mathematics and bioscience block on the land.