Extensive information about contaminated rivers can be found in the "Urban Water Blueprint," a 64-page report published in 2014 by The Nature Conservancy. For a brief overview, in July 2013, Eric Zerkel posted an article entitled "The World's Most Endangered Rivers" on weather.com.
The above cited sources discuss specific cases while the EPA discusses general causes in an article entitled "Nonpoint Source Pollution." These causes include runoff from construction sites, agricultural chemicals, pesticides and pathogens. Finally, the American Museum of Natural History posted "River Ecology," which captures the dynamics of waterway health in a report on the effects of the invasive zebra mussel on the Hudson River system.