Not sure about the specifics in this particular case, but here are common things that contribute to poor river water quality:

• Impermeable surfaces in human-built environments, which cause water to flow more quickly and therefore erode river banks (dams and retaining ponds help slow down water flows)
• Residential and agricultural fertilizer/manure runoff, increases nutrients in water that cause microbes to grow faster
• Tiling agricultural fields, which releases more of the above
• Untreated human sewage
• Improper dumping of industrial chemicals, or breach of containment due to upstream flooding
• Runoff from abandoned mines