A father-and-son team of British documentary film-makers has discovered the long-lost source of an ancient Roman underground aqueduct beneath a ruined medieval chapel near Lake Bracciano, 40km north of Rome.

Edward O’Neill, 37, and his father Michael, 64, who are jointly making a documentary on Rome’s aqueducts, said local memories combined with clues in historic accounts of the Aqua Traiana, the aqueduct built by the Emperor Trajan (reigned AD98-117), had led them to the chapel hidden in undergrowth in a field on a pig farm at Manziana, near the lake.

Professor Lorenzo Quilici, an archeologist at Bologna University, confirmed that the ruined chapel, called by local people the chapel of the Madonna of the Flowers, was Roman in origin. He said it was a nymphaeum dedicated to the Roman water spirits at the time of Trajan.

It has diamond-shaped criss-cross patterned brickwork typical of the period, known as opus reticulatum, and a vaulted ceiling painted with a rare and valuable paint called Egyptian Blue, which now has fig tree roots growing through it.

Edward O’Neill said the vaulted nymphaeum marked the headwaters of the Aqua Traiana, the stone channel that carried spring water from an aquifer to many districts of Rome. It was inaugurated in June AD109, possibly by Trajan himself, who is recorded in the area at the time.

O’Neill Jr added that a coin minted under Trajan showing a god of the waters with an urn and a reed reclining under a broad arch almost certainly represented the nymphaeum at Manziana. He said that the local councils at Manziana and Bracciano hoped to buy the pig farm land and excavate the site. “The chapel and aqueduct are in danger of collapse and need to be urgently restored,” he said.

The O’Neills said they had also consulted The Aqueducts of Ancient Rome by Thomas Ashby, director of the British School at Rome from 1906 to 1925. Ashby had not found the source of the Aqua Traiana, but had provided valuable clues from ancient writers, Michael O’Neill said.

He said water from the aqueduct supplied the first shrine, later basilica, dedicated to St Peter after Rome began to convert to Christianity under the Emperor Constantine. This explained why the nymphaeum at the aqueduct’s source was converted into a chapel, which may have existed much earlier than the 13th century.

The aqueduct fed a complex of water mills that were arranged in a parallel sequence on the Janiculum Hill (beneath the present American Academy in Rome) but that were destroyed by the invading Ostrogoths when they cut the aqueduct in the 6th century. The Aqua Traiana fell into disuse when the Western Roman Empire disintegrated. It was later restored by 17th-century popes, including Paul V (reigned 1605-1621), who built the fountain known as the Fontanone di Acqua Paola on the Janiculum Hill above Trastevere in 1612 to mark the renovation. However the source, concealed by undergrowth, was gradually forgotten, although local memories of it survived.

A modern water pump still extracts 5,000 cubic metres of water a day from a nearby borehole. The extraction has caused a lowering of the water table “with the effect that rapacious fig trees and other species are sending long powerful roots down into the subterranean chambers and causing considerable damage to the wall plasters and mortars,” Edward O’Neill said. “Without remedial attention this structure which has existed for over 19 centuries could collapse just a few years from now.”

He said the documentary team, supported by the Rome provincial council, was appealing for financial help for restoration and conservation.

Rabun Taylor, assistant professor of classics at the University of Texas at Austin, said Trajan’s aqueduct originally reached not only Trastevere but also the opposite side of the Tiber, curling round the Aventine Hill to reach the Colle Oppio above the Colosseum, the site of Trajan’s Baths. He said this was proved by the discovery of lead pipes stamped with the name of the aqueduct.