[vitaminj]

This guy built a classic run-of-the-river scheme, i.e. the main stream is not dammed. He built an intake channel off the main stream that flows into a forebay, where the penstock and piping system is installed. He also talks about putting a trash filter in the forebay, again a pretty standard thing to do.

Run-of-the-river schemes probably have the lowest impact on the local environment. I'd imagine very few fish would go into the intake channel.