It's changing slowly but large livestock operations used to spread manure where it was convenient, not where the extra fertilizer was needed. Now they're required to file plans, complete with soil tests to show they're putting the manure where it's less likely to be a problem.
When I left the fertilizer business over twenty years ago we were helping the large livestock farms begin composting. If you rid the manure of it's largest component which is water then hauling a load to a distant field is way more possible.
Hard for some to believe but people who sold fertilizer were encouraging there customers to use less! Imagine a car dealer telling you not to buy an additional car.
The government also had a program where they would pay farmers to plant grass strips along waterways with the idea the strips would intercept the nutrients from fertilizer or manure before they reached the water. However I believe funding for that program was cut which may be adding to the problem.