As y'all may know, the Geothermal Generators can be ran using either Lava Cells, Lava Buckets, or by connecting a Buildcraft Waterproof Pipe to it and feed lava to it. When it comes to the Water Mill, it can generate EU by either being surrounded by water to create water towers, or be fed water buckets.
My suggestion is for the Water Mills to have Buildcraft compatability, just like the Geothermal Generators, so that you can supply a Water Mill with water by using the Buildcraft Water Pipes. It would require no additional recipies, but just the ability to connect a BC Waterproof pipe and be fed water from a source. As well as generating the same amount of EU if fed water buckets or sunken in water and surrounded by a 3x3x3 cube of water.
This all boils down to one thing: if the Geothermal Generator can generate EU by feeding it with lava from the BC Waterpipes, you should be able to do the same thing to the Water Mills.