That is strange. If you use the Flow Restructure device and directly afterwards the Create Water device, it shouldn’t be able for rivers to flow uphill. In general, the Create Water device will not create rivers that flow uphill, but if you take the water output and, using the Scene View device, lay it on top of a different terrain, you can get “uphill” rivers, so my question to you is, does your node setup in essence look like below, or is something funky going on?
