This is an excellent article written by Bobby Whitescarver from Swoope, VA on the importance of planting native trees and shrubs adjacent to waterways to improve water quality.
Nature intended for trees and shrubs to grow next to streams and rivers. Vegetation stabilizes soil, decreasing erosion and the associated impairment to aquatic microorganisms. Trees provide food and habitat to stream-dwellers as leaves and other organic matter drops to the water below. Trees also shade the water, decreasing water temperature which many species, like native brook trout, require.