I have an idea which would solve many of the water usage versus riverine health dilemmas. It is very simple.
In stead of allowing farmers to take water directly from a river have them drill a bore next to the river. That way they access water from the saturated soil next to the river (water that has already left the river system) while leaving the river untouched. If government were to fund the drilling of these bores (they need only be shallow) it would be a win-win for both farmers and environment. Hope you can understand that this is a simple and feasible thing.