Ag pollution is not profitable to the farmer. Manure may be a by-product of livestock, but it is also an input for crop farming whereas in industry pollution is a cost to get rid of as cheaply as possible. If you come to my farm, test the water, and find nutrients that have come from my farm then I'm losing money. That is also true with pesticides. This is why nonpoint Ag pollution control can and should be handled differently than industrial pollution.
Funding is the major problem with trying to improve water quality today.
This administration has replaced funding of government programs that actually clean up the environment and reduce possible contamination with programs that educate the general public and create more government bureaucracies. The current EQIP funding for New Hampshire is less than half of what the old ACP program was. However, the Connecticut River is listed as a Historic river and Silvio Conte is building learning centers. Not only has funding levels gone down but bureaucracy has gone up. Money is made available by priority water shed, within which watershed projects are rated, for environmental impact.