For a century, the confluence of the Clark Fork and Blackfoot Rivers was submerged by the Milltown Dam Reservoir. The state's mining legacy left more than 6.6 million cubic yards of mining waste, laden with heavy metals and arsenic, in the sediment behind the Milltown Dam. The contamination, much of which washed downriver from Butte's mining district during a massive flood in 1908, polluted the community of Milltown's aquifer with arsenic. Additionally, the dam itself blocked a critical migration corridor for the threatened native bull trout.

After more than twenty years of study, planning, and legal negotiation, the work on one of the nation's largest Superfund cleanups began in the fall of 2006. More than two million cubic yards of toxic sediments and the dam and associated structures were removed.