Gah!, I haven't played that in years, I loved that game!
I think that you'd have to use sprite tiles anyway, like pipe sections to make up the maps, so manually drawing the water is probably the easiest option. Like if you had 8 different bits of pipe, maybe make 16 copies and add a little water each time, if your pipe section is 16x16 pixels, then 16 frames would fill the pipe up nice and smooth.
With your map array, you would have another array for the amount of water, and with this you can increase the water amounts, when one get's to the last frame, like full of water - you can check the type of pipe and decide where the water spreads to.
Van-B

Put away, those fiery biscuits!