a good thing you're concerned about the ecosystem,not everyone is.

I was thinking about a floating ball or something like that,that shuts the 4" inlet pipe when level is low.
The problem will be to have enough 'floating force' to pull the ball off against the   negative pressure when level is rising,however you can calculate this.

You have to place the inlet in a wider place in the stream with a narrower outflow.
So you have a place were the flow in the stream is calm for not having to much sand going in the inlet, and where level will rise significantly with increased debit.

Just my thoughts.