I swear it's flowing uphill, but in a very beautiful manner.
I really think that's just a mind-trick because of a games inability to actually create a true sense of depth perception. Regardless of how the graphics are presented, you're still always looking at a 2D plane drawn in 3D, which doesn't always translate in the human brain.
Anyway, I still have on big issue with the water in General, and I haven't seen a lot so maybe it is different now, or somewhere else, but the "Hard" Water edges bug me. Morrowind's MGE solve the issue with Shader 4.0 (I think?) for their water, making it actually roll over the pre-defined water's edge, though this created some issues in parts of the game where the land isn't far enough above the water line, and waves clip through the ground.
Still, it really sells the "Shoreline", which was a surprisingly big touch, especially in a game with so much water.