I would say just have the water animated in the models. Like have the pipe at empty be frame 1 or something , then on have a filling with water animation , and a full animation, then when you rotate the pipe or something and it gets the right position , have the filling animation start , then when it's done have it switch to the full animation. To animate the water you can just have the water cylinder inside the tube pipe, just position it where the pipes connect so you don't see it , and scale it's length to something like 1, then hit the button to animate and move to frame 10 or something and scale it so it fills the whole tube(animation process depends on program your using for the models, but it should be similar). Hope it helps.