Alan S. Kesselheim's lead story on the Yellowstone River hits the nail on the head (HCN, 3/27/00: The last wild river). A classic, one-of-a-kind, free-flowing river gets ruined because of greed and stupidity. The fact that anyone can build anything in a 100-year floodplain is insane. Look at the Mississippi if you want to see what happens when a natural river is channelized with nowhere for the water to go during floods.
Also, a friend of mine saw a fisherman pull a pike out of the Yellowstone River last week. Add that to the problems with whirling disease and you have another problem of immense proportions.