In 1995, the Environmental Working Group published an article Weed Killer by the Glass, a report that showcased that there were nine different herbicides found in Fort Wayne’s drinking water. Fort Wayne had the second-highest level of atrazine in its tap water of all the cities identified in the report.

Citizens, concerned about this report, organized a partnership with various agencies within the St. Joseph River's three-state watershed. In March 1996, the newly formed group brought together local and state natural resource professionals and political leaders to share information and discuss issues and solutions to water quality issues. At the “Conference on the St. Joseph,” participants provided the guidance and motivation to drive the development of a strategic plan. After the “Conference on the St. Joseph,” the group formed a steering committee to develop the organizational structure of the St. Joseph River Watershed Initiative.

The first Board of Directors was formed in April 1998 and was incorporated in October 1998. On January 21, 1999, the Internal Revenue Service designated the Initiative as a 501(c)(3), not-for-profit organization.

Since its formation, the group has brought over $4 million to protect, restore, and enjoy the St. Joseph River and its watershed, which stretches across 694,400 acres through six counties in Indiana, Ohio, and Michigan.