The Baltic sea is relatively new in the grand scheme of things. It was formed the receding Glaciers around 10,000 - 15,000 years ago.
This would not be the first settlement found under the water in this region. I was reading that there have been stoneage settlements found closer to the Swedish coasts which would have been last inhabited around 11,000 years ago.
I used to suspect this theory, but I always found the drag marks in the sand to be out of place and hard to explain.