I had a water pump placed in water when I added this mod. I also have an old version of Waterfill left enabled by mistake.

When I loaded my save, the existing water pump stopped pumping, when I removed it weird things happened to the mouse input for a minute but it cleared up. I believe removing and replacing the water pump fixed the issue.

Otherwise great mod! Thanks!

Can you send me the save file so I can see what happens?

Never mind, I got it to happen in my own. I think I fixed it, just need to test a little more.

I tested by placing pump in a lake (new game) with a few pipes attached, built with mod disabled. After enabling the mod, the pipes still have water; last time I think they didn't. Seems like it might be fixed?
Thanks so much!