Yeah, looks like the waterwheel in the river turns the right way now.

But the wheel inside the Mill still turns counter-clockwise. Also, about twice as fast.

Hmmm... Maybe there're some gears outside, behind the water-facing wall?

I honestly don't see an issue. Everything appears to flow southward, with a correctly propelled water wheel spinning with the current. 

https://m.youtube.com/watch?v=Vl80HrDMKPk

 

Much smaller but maybe explains the speed inside?

The mill is pushing the water, obviously.

Hilarious mistake! Then again, you don't see the start or end of the river in the ingame world-map. It could come from a mountain, go northwards until it hits the other river or flow into an underground cavern.