When you measure the levels of nitrates/phosphates etc in rivers, you can't differentiate from whence it comes. What I'm illustrating is that it was previously unknown just how much water companies were dumping in rivers with most of the blame being targeted at agriculture.
I'm not for a minute suggesting that all farmers follow the rules all of the time, but there are very onerous regs about where and when you can fertilise and how muck must be stored (for example, nothing within 10m of any watercourse, no spreading when the ground is frosty etc etc). The penalty for breaking these means as well as legal implications, you'll be failing on your cross compliance, which will mean subs are docked, and you'll lose your Red Tractor status (or whatever other FABBL you have, RT is the least onerous). In some sectors (arable, pig and poultry, dairy) that means you'll have almost no market for your produce and therefore it can bankrupt you.