The floodwaters have not arrived yet but the Yortanli dam is ready. As his team of tireless diggers ignores the sizzling Anatolian heat to uncover the secrets of Allianoi, Dr Ahmet Yaras had the look of a condemned commander about him.

It would, he said, be death by drowning for the world's oldest known thermal spa. "And still," he exclaimed, his eyes scouring the wooded hillocks of the ancient settlement, "there is so much to find."

Days after Turkey's government gave its blessing to the construction of the controversial Ilisu dam in the south-east of the country, archaeologists in western Allianoi have accelerated efforts to salvage a 1,800-year-old health centre that is arguably the most impressive and best preserved on the continent of Europe.

Not since excavations began in 1998 has the quest to unearth the mysteries of the complex been so fraught with the knowledge that time is running out. The Yortanli project was completed last November and only pressure from both inside and outside Turkey has kept the floodgates closed.

Laying the foundation stone for the Ilisu plant - a project that campaigners claim will wreak "cultural mass destruction" on the historic site of Hasankeyf while displacing thousands of Kurds - the Turkish prime minister, Recep Tayyip Erdogan, summed up the dilemma thus: "On the one hand, you have the increasing demand for energy and a bright future for Turkey; on the other history, culture and an inheritance that belongs to all humanity. We have to find a solution. We have to make peace between the two sides."

In Hasankeyf, on the banks of the river Tigris, authorities have earmarked €25m (£16.9m) to relocate antiquities that include Assyrian, Roman and Ottoman monuments despite the idea being dismissed as risible by experts.

But in the case of Allianoi, an assortment of monumental streets, squares, churches, bridges, gates, fountains, hot springs and stores, such measures are impossible to take. "You can't remove any of the monuments there," says Gunhan Danisman, the vice-president of the Chamber of Architects in Istanbul. "The only way to save them is to stop the dam filling up."

The ruins of Allianoi are among the few "asclepions" - or therapeutic centres - ever discovered. Testimony to the extraordinary sophistication of urban planning and hydrological engineering during the Roman era, archaeologists believe that with its curative waters, the spa city complemented the legendary asclepion at nearby Pergamon. There, patients were healed through psychotherapy to the accompaniment of music.

Artefacts found on the site, including bronze surgical instruments, suggest it was a prominent health centre from the second century BC to the 11th century AD. Having survived earthquakes in AD 178 and 262, the site has been spectacularly preserved beneath alluvial soils.

But it would not withstand the waters of the Yortanli dam. Lying at the centre of its reservoir along the Ilya river, officials and archaeologists agree that with the opening of the flood gates the antiquities will be immediately submerged. Once inundated, an estimated 12-15m of silt will cover the city.

The irrigation project was first proposed in 1970 to benefit fewer than 6,000 farm families in the region. Fed with the extra water, fields that presently produce single crops of cotton, tobacco and melons should yield several harvests a year.

"In Bergama [Pergamon] there is no industry and unemployment is a big problem," says Hasan Astarlar, a member of the town's municipal council. "Farming is the only way out but our fields don't have enough water. There are no irrigation canals, another big problem when the weather in recent years has become so hot."

But the town of 52,000 people is divided. Some 500,000 tourists visited Allianoi last year. Locals realise that while the technology exists to build modern dams, it cannot "make the past" and the sort of monuments that draw the crowds.

"History is very important for Bergama," Rasit Urper, the bustling town's moustachioed mayor, told the Guardian. "Building the dam was very expensive. It's not something we can just ignore now, but we also believe that Allianoi should be saved. Our hope is that we'll be able to build a protective wall around it with the help of the international community."

So far, that option has been ruled out on the grounds of being more costly than the dam itself.

Opposition to the project has mounted both at home and abroad. Last year, the EU's top enlargement official, Olli Rehn, warned that the destruction of the site would not only result in "irretrievable loss to the cultural memory of Europe" but also reflect badly on Turkey's image as it negotiated EU membership.

Under pressure, Turkey - a secular state governed by an Islamic party - has deferred opening the dam, but with crucial elections next year, and the battle for votes along the country's traditionally liberal Aegean coast a priority for the conservative government, fears abound that political expediency may win the day.

"Turkey doesn't love its archaeology," says Dr Yaras, wearily shaking his head. "All over this country there are dam projects that pose similar problems for archaeologists, but with this government we have the added problem that it only values monuments from the Islamic period. I worry that with elections coming up, the Yortanli dam could be turned on overnight."

Should that happen, campaigners say they will have to store their hope in technology enabling future generations to unearth Allianoi again.

"All dams after a certain time fill up with alluvial soil," says Professor Danisman. "My hope is that in 35 years, say, excavation techniques will have become so sophisticated that we will be able to discover Allianoi under the earth again."