The Chicago Area Waterway System (CAWS) connects the Great Lakes watershed with the Mississippi watershed via canals that withdraw water from Lake Michigan. From 2009 through 2011, collaborators and I provided research, development, and application of eDNA to invasive species management in the CAWS in cooperation with the US Army Corps of Engineers (USACE). The research team's approach was a high‐stakes test of a novel combination of proven technologies (field sampling techniques and laboratory genetics). In the first application of eDNA to a large scale, urgent management goal, we quickly discovered eDNA of two species of bigheaded carps in parts of the waterway where traditional tools had not captured fish. The central research question was whether the sensitivity (probability of detecting a fish when it was present) of eDNA was higher than that of traditional fish sampling tools (e.g., nets, electrofishing). The effort was part of what became a very large, complex, on‐going initiative to reduce access by invasive species to Lake Michigan. This immediately garnered much attention, initiating a dialog about the reliability of eDNA, public discussion about the benefits and costs of the CAWS, and skepticism from industries that use the CAWS. Government agencies formed the Asian Carp Rapid Response Workgroup, which eventually became the Invasive Carp Regional Coordinating Committee (ICRCC). The ICRCC continues its coordinating role on the use of eDNA and other management responses in the CAWS. With the benefit of hindsight, I draw several lessons from the experience that may help in other settings where eDNA is now being deployed with increasing confidence and acceptance; evaluate the on‐going CAWS surveillance and management effort; and recommend strengthening the current approach by broadening and deepening participation in a collaborative governance approach. Stronger public‐private partnerships would accelerate research, development, commercialization, and application of eDNA analysis to the benefit of society.