Allianoi, an ancient site that was discovered just 10 years ago, will be submerged under the waters of Yortanli irrigation dam, which is much needed for the local farmers.
When construction of the dam began in 1998, the archaeologists, as a routine procedure, were asked to make a survey of the land.
Local people knew about and used a thermal spa centre called Pasa Ilicasi, which had been there since the Ottoman Empire.
But nobody knew that this place was actually a Roman asclepion (ancient healing temple) dating back to second century AD.
The then manager of Bergama Museum and leader of excavation team, Ahmet Yaras, found the site.
"Once we realised that it had an enormous cultural heritage and a beauty, we continued excavations despite the planned flooding," he explained.
"We found the best preserved thermal spa from the 2nd Century AD, but unfortunately they haven't stopped the dam project."
For almost seven years there have been arguments and debates about the future of the site.
Finally, last September, the Ministry of Culture and Tourism decided to go ahead with the dam and protect the archaeological site by simply surrounding it with a wall and covering it in clay.
Government officials that say if the dam can collect enough water from the spring rains, then they might flood the land before this summer.
Because Allianoi is spread over 40,000 cubic metres, Mr Yaras said that the team had not excavated surrounding parts of the site.
"We, the scientists, aim to reach the knowledge. Whether the government decides to protect these sites or open them to tourism is up to them.
"What makes us sad is that before we reach the knowledge, a cultural heritage is being destroyed.
"It is not Turkey's knowledge, it is universal and obstructing people from reaching the knowledge is a crime against humanity."
According to the archaeologists, if you check the history books you come across the word Allianoi (the name of the town) in only one book, called "Hieroi Logoi", or "the Sacred Tales", written by Aristides.
In this book, he says: "on my way to Pergamon (sometimes called Pergamum), I came across a thermal place.
"I had a sore throat, so I took a bath and I prayed to the God Zozimos. Then I was cured... and this place was called Allianoi."
But the Water State Authority officials insist that the place found is not actually what archaeologists say it is.
According to an industrial engineer, Ahmet Tomar, who works for the government, this place had been and known as Pasa Ilicasi since Roman times.
"Wherever you chose to build a dam in Turkey, you would come across an archaeological site as well," he said. "By development-led excavations we rescue the most precious artifacts."
The Bakircay river basin project was originally planned in the 1960s, but not actually finished until 2005.
The engineers of the Yortanli dam say the water gathered by this and one of the other dams being built nearby will irrigate 18,000 hectares (44,000 acres).
According to them, people here need water desperately.
The villagers in the area, many of whom earn their living from agriculture, have mixed feelings.
Tomatoes and cotton are the most produced crops around this region. These crops need more water than any others and, especially during summertime, it gets difficult as most of the rivers around the area dry up.
Some villagers longing for water for their fields believe that the region will become wealthier than it could through tourism. Others insist that if Allianoi is opened to tourism, they will benefit more.
Some villagers have been paid by the government to leave their homes that are located within the area to be flooded.
A village head says: "Money is not always the most satisfying thing. We earn our living by breeding animals in the fields.
"I am sure it is very beneficial for our country but not for our village."
Turkey has a rich history beneath its soil, but it is also trying to boost its economy to be ready for entry into the European Union.
This dam project itself has caused a diplomatic war of words between Ankara and Brussels.
Turkey has wanted to join the EU for more than 40 years, but people who want to preserve Allianoi argue that its destruction is in conflict with EU rules on preserving ancient monuments.
They hoped that the EU would raise strong enough objections to make the Turkish government change its mind.
However, the EU's objections so far, have been ineffective.
Greek Socialist MEP Stavros Lambrinidis asked a question at the European Parliament (EP) about Allianoi earlier this year.
Lambrinidis says he wanted to know "what the EP was planning to ensure that the Allianoi will not be flooded without any concrete and scientifically justified measures to protect it."
Cem Ozdemir, a German MEP of Turkish descent, also quizzed the European Commission about the plans.
"Imagine the Tower of London being destroyed by British government," Mr Ozdemir says.
"It would be beyond British interests, it would raise worldwide awareness. I believe Allianoi deserves same kind of awareness."
The legal cases opened to save Allianoi are still ongoing. The Allianoi Initiative, an NGO which supports the protection of the site, has decided to approach the European Court of Human Rights on this issue.
They are demanding permission for the excavation team to continue their work for another five years.
The group is also hopeful that there might be a solution, maybe a legal challenge that can still save Allianoi, but in theory the clock has stopped ticking.
The government can start flooding this ancient site anytime.