As far as I know, Prague ended up under a mud flood several times, not a water one.
But what if it's true and it really was "just" a water flood. In the Krkonoše Mountains, where I grew up, there is still about 3m underground in the forests sea sand. There are also many fossils of trilobites (to me it looked more like huge fossils of beetle bugs - about 5-10cm in diameter).
If the ocean or the sea was in the mountains Krkonoše, then Prague, which is in a hollow, must have been underwater as well. But that would mean that all the structures in the deep underground of Prague were not built by the current civilization, but by a completely different one. And the mud deposits were caused by receding water. But this can't be anything complicated to find out if there was salt or fresh water below, based on the damage to the building stones. It's all over Europe and all the politicians know it-every time something was found, the order was to bury it, I know this places.