This sounds like the first act of a Mythos story, but it's absolutely true.
In the late 1950s the governments of Romania and Yugoslavia decided to move forward with the Iron Gate hydroelectric dam. The project would create a massive artificial lake, impounding the water of the Danube and flooding the banks of the river. Archeologists started to survey the soon to be inundated areas and discovered evidence of a previously unknown culture dating back to 7000 BCE. The buildings were arranged in a complex geometric pattern, and excavations uncovered dozens of idols depicting human/fish hybrids. Even stranger, it's the only European site where a "double sunrise" astronomical alignment has been found.
Author Dan Davis has a great look at the Lepenski Vir site over on YouTube. It's just the thing if you're looking to incorporate some real-world inspiration into a Mythos scenario. You can find even more information, including the effort to relocate the entire complex above the flood line, in the Wikipedia entry.






