I have not had the opportunity to fish any of the waters discussed but I must agree that stream and river degradation is a direct result of livestock entering and defecating in the water. Excess silting, the introduction of bacteria and nutrients, lowering of water quality and general destruction of the streambed and surrounding lands are all symptoms of livestock allowed in the water.
One of the best groups that work with local farmers and residents is the Grand River Conservation Authority in Southern Ontario, Canada. They govern the Grand River which flows 300 kilometers from source to Lake Erie and all of its tributaries and water sources. They have been working with local farmers and providing grants to improve water quality. One of the best methods is to provide fencing away from the water. This not only improves the water quality and associated benefits (improved underwater life, both insect & fish) but it can also provide an access route for the angler without disturbing the local livestock.
This has providing some excellent fishing opportunities for Brown & Rainbow trout and smallmouth bass not only as a result of the above but also through special regulations on some of the waters.
All of this in one of the most heavily populated areas in the country.

http://www.grandriver.ca/index.cfm

Check out the resource management topics i e rural water quality and the examples of what can be done.