The 319-mile (513 km) route runs from Chicago, Illinois, to Port Huron in Michigan's Blue Water Area, for which the train is named.

Beginning in 1973, Amtrak and the state discussed restoring service over the Grand Trunk Western Railway within the state, although the new route would join Amtrak's other Michigan trains on the Penn Central west of Battle Creek, Michigan, eschewing the Grand Trunk's traditional route to Chicago.

Massive border delays post-September 11 led to falling ridership; Amtrak and Michigan agreed to truncate service at Port Huron and bring back the old Blue Water.

With a more favorable intrastate schedule and fewer delays, the Blue Water's ridership showed immediate improvements, carrying 94,378 passengers in fiscal year 2004 (compared to 80,890 in FY 2003).

[8] A 97-mile (156 km) stretch along the route of Blue Water from Porter, Indiana to Kalamazoo, Michigan is the longest segment of track owned by Amtrak outside of the Northeast Corridor.