The original need of the Commission was to prevent abandonment of the bankrupt Milwaukee Road rail line between Madison and the Mississippi River at Prairie du Chien, including the branch lines from Mazomanie to Prairie du Sac and from Lone Rock to Richland Center. Since then, the WRRTC has been granted the responsibility of protecting and preserving other rail corridors throughout southern Wisconsin.

Six counties were included when WRRTC was created: Crawford, Dane, Grant, Iowa, Richland and Sauk. Rock and Walworth counties joined in 1982 when WRRTC purchased the line from Madison to Fox Lake, Illinois, via Janesville. Waukesha County joined in 1987 when WRRTC purchased the line between Milton Junction and Waukesha. Richland County left the Commission in 1988 when the line from Lone Rock to 
Richland Center was abandoned.  Jefferson County joined the Commission in 2014.

 A brief history
  • In December 1978, the Lone Rock to Prairie du Chien line was filed for abandonment by the Milwaukee Road Railroad. 
  • In 1979 - 1980 studies were initiated to determine possible options with regard to retaining rail service on the Lone Rock to Prairie du Chien and the Madison to Lone Rock/Richland Center line segments. During this same period the counties of Crawford, Dane, Iowa, Grant Richland and Sauk were meeting to discuss possible actions to preserve rail service. 
  • The Wisconsin River Rail Transit Commission (WRRTC) was formed in March of 1980 by the counties of Crawford, Dane, Grant, Iowa, Richland, and Sauk. It was determined that the only viable option for saving the Lone Rock to Prairie du Chien portion of the line was to acquire and operate the entire Prairie du Chien to Madison line. It was anticipated that it was only a matter of time before the Milwaukee Road would pursue the abandonment of the Middleton to Lone Rock/Richland Center segment, so the WRRTC worked with the Milwaukee Road and the Wisconsin Department of Transportation (WisDOT) to achieve a friendly abandonment. Despite efforts by some commission members to acquire the track all the way to Madison, the Milwaukee Road would only abandon and sell to Middleton. 
  • The WRRTC advertised for rail operators interested in the system in October of 1980. The Wisconsin Western Railroad was selected in July 1981 as the top candidate and contract negotiations began. The Wisconsin Western group was lead by John Zerbel. The Zerbel group also owned the Central Wisconsin Railroad, which operated the Waukesha to Milton Junction track. The Wisconsin Western agreed to provide the $488,000 local match needed to purchase the line. Operations began in the summer of 1982. 
  • In June of 1982 Rock County joined the Commission and the Commission took action to expand its jurisdiction to include the Janesville to Madison line owned by the Milwaukee Road. 
  • In 1982 the Chicago Madison & Northern Railway, which operated the lines between Madison and Freeport and Janesville and Mineral Point filed for bankruptcy. The Central Wisconsin Railroad/Wisconsin Western Railroad was selected as the successor operator. Using trackage rights from the Milwaukee Road in Madison and Janesville, all segments were connected and operated as one system. 
  • In February 1983 the Walworth County Board acted to join the Commission, and the Commission became actively involved in the Janesville to Fox Lake line. 
  • In 1984 John Zerbel died and in December 1994 the Wisconsin Western and Wisconsin Central Railroads filed for bankruptcy. The entire rail system was closed until a new operator could be found. 
  • In January 1985 the Chicago West Pullman Railroad assumed operations on the Janesville to Mineral Point and Madison to Freeport, Ill rail lines. The Wisconsin & Calumet was formed by the Chicago West Pullman to operate the Wisconsin system. The Middleton to Prairie du Chien line was not operated again until the summer of 1985, when the Wisconsin & Calumet resumed service. 
  • In 1987 Waukesha County joined the Commission and the Commission assumed jurisdiction over the Waukesha to Milton Jct. rail line.  
  • In 1988, Richland County left the WRRTC when the line from Lone Rock to Richland Center was abandoned.
  • In August of 1992 the Wisconsin & Calumet was acquired by the Wisconsin and Southern Railroad (WSOR). 
  • In 1994 WSOR acquired the Madison to Middleton track from the Milwaukee Road. Discussion continued regarding the eventual state/transit commission ownership of the line. 
  • In 1995 WisDOT provided WSOR with a grant for the acquisition price of the Madison track and in return WisDOT received an option to buy the trackage at a future date for $1. 
  • In 1996 WSOR completed a lease arrangement with the Union Pacific for branch lines between Madison and Reedsburg, Madison and Cottage Grove and Madison and Fitchburg. 
  • WSOR assumed operations in 1998 on the Madison to Watertown line under a lease agreement with the Canadian Pacific Railroad.
  • In 2012 WSOR entered into partnership with Watco Transportation Services, L.L.C. 
  • Jefferson County joined the WRRTC in January 2014, becoming the ninth county in the Commission.