It's probably a limitation due to how the game is designed. Water level is "global" and can't be changed locally, so the river/lake altitude is always sea level. I agree it isn't great, but there it is. Many games do it like this. As for building on deep water, the only thing you can do is try to raise the riverbed/ocean floor with stone. I was able to create an partially enclosed dock for my ships off the coast so they were less susceptible to attacks, but because the waves go through solid objects, it doesn't mellow out the water inside. Thankfully the ships aren't shifted around except vertically.

You can benefit from keeping all that stone you find and storing it in piles.