As the EPA continued the cleanup of the Superfund site, the State of Montana began to implement a restoration plan to return the river to a similar state that was there a century ago by reestablishing natural stream channels and native vegetation. Restoration is the reshaping of the floodplain once the cleanup is accomplished. Many factors are included: elevations, terracing, revegetation, the river channel. A successful restoration would restore a naturally functioning Clark Fork River.

The design of the channel and re-vegetation was planned after extensive studies by a Restoration Team composed of the River Design Group, Westwater Consultants, Geum Environmental Consulting, EPA, the Confederated Salish and Kootenai Tribes, Envirocon, and NorthWestern Energy working closely with the Montana Department of Justice, Natural Resource Damage Program.

Funding for this work came from the 1999 partial settlement in a lawsuit involving ARCO, the responsible party for the damage. The settlement earmarked about $130 million to restore or replace the injured natural resources in the Upper Clark Fork River Basin.

In November, 2005, The Confluence (PDF), newsletter of the Friends of 2 Rivers reported on the draft Restoration Plan.

"Restoring rivers to 'a naturally functioning, stable system' a challenging goal," by Doug Martin, Pat Saffel, Gary Decker, and Tom Parker was reported in the Friends of 2 Rivers newsletter, September, 2006 (PDF).

Project Manager Doug Martin outlined the Final Restoration Plan features in the Friends of Two Rivers newsletter, The Confluence, June, 2007 (PDF).

In 2008, restoration work began in earnest. Friends of Two Rivers newsletter, The Confluence, November, 2008 (PDF).

In April 2009, Tom Parker discussed the progress of the revegation plan. (Friends of Two Rivers newsletter The Confluence, April, 2009, pg. 4, PDF)

Doug Martin, project manager for NRDP, gave this report at River Restoration Northwest in 2013. (PDF)

In September 19, 2015 the Missoulian published an article "Milltown floodplain growing strong five years after Superfund cleanup."