Any gaps can be filled by Silicone or if you hot dip galvanise it small gaps will be sealed in the process. Slide the piece of round pipe through the holes in the flanges and weld into position. To fix the wheel into its final positon, simply slide it onto the drive shaft and bolt into place. To protect the wheel from rust, you can paint it with cold gal metal paint or get it hot dip galvanised. Alternatively don't treat it at all.
Steel rusts very slowly when it is kept wet.
The water supply The water to run the water wheel comes through a six inch steel pipe from 100 metres upstream. To keep rubbish out of the pipe water enters it through a slotted section, while a valve in the pipe controls the water flow. To help protect the wheel from flooding, David cut a back water in the bank of the creek. The water wheel was connected to both a generator and a water pump. It took a bit of trial and error to get gearing and load on the water wheel just right.