I agree that’s a problem, however unlike most environmental issues runoff is an inefficiency not a byproduct. Farmers that more efficiently use fertilizer directly have less runoff. So, generally the economic incentives are in close alignment.

The US for example has seen a significant reduction in runoff without that much pushback from farmers. That said, there is a point where with wasted fertilizer costs less than the methods of avoiding runoff, which changes the dynamics.

You can have nitrogen runoff problems whether you use artificial fertilizer or manure, the only difference is that people who use manure typically (though not always) are more careful about it.