My pond is mostly filled by an adjacent stream.
If you try to put a screen across in the inlet pipe, in the stream itself, you will constantly have to clear the screen of debris. It's not such a big deal, and more a labor of love.
Regarding rough fish getting in from the stream, I think that will be very, very difficult. You'd have to filter against the smallest of fry getting into your pond, and to do so, you'd have to have a fine filter which would get clogged very easily.
I'm not saying it can't be done, but you might spend a lot of effort trying to keep a 'pure' fishery and still get rough fish.
Personally, I just accept the nature of my pond for what it is, and enjoy the diversity.
