General oversight of the Initiative is provided by the National Partnership for the Management of Wild and Native Coldwater Fisheries. The National Partnership is a consortium of organizations concerned with the status of wild and native fisheries in the United States—Federal and state agencies, professional associations, and private advocacy organizations. The overall goal of the Partnership is to move biological research and management trials forward to make available to fishery managers practical options for controlling the disease. The National Partnership provides long-term direction to the Whirling Disease Initiative. To do this, the Partnership’s Board of Representatives convenes periodically for a detailed briefing by whirling disease researchers, and discusses fisheries health and research needs.

In-depth scientific direction is given to the Whirling Disease Initiative by its Steering Committee. The committee is made up of representatives from state fish and wildlife agencies, Federal natural resource agencies, and Trout Unlimited (formerly the Whirling Disease Foundation). Working in collaboration with Montana Water Center staff, the Steering Committee prepares research plans, issues Requests for Proposals based on its topical priorities, selects and approves projects for funding following scientific peer review, and distributes the research results within the scientific and fishery management communities and to other stakeholders. The Montana Water Center is the administrative entity that manages the program and coordinates outreach and educational activities.

Each year from 1997 to 2006, Federal funding earmarked in the Interior Appropriations Bill came to the Initiative through the Division of the National Fish Hatchery System, US Fish and Wildlife Service. Projects were chosen for funding by the Steering Committee, following peer review by three or more independent reviewers. During this period, the Steering Committee chose to support a variety of projects, ranging from basic biological research to applied research directly testing potential management solutions. Early projects were principally aimed at explicating the biology of whirling disease. In 2000, the Steering Committee began deliberately shifting the priority toward field research more closely tied to possible management strategies. In the final (2006) round of new projects, this “applied” focus led to large-scale field projects addressing the effects of whirling disease on fish populations, and their possible recovery.

Between the years 1997 and 2006 the Initiative sponsored as many as 20 research projects in each cycle. A research cycle generally ran from May of one year through December of the following year, allowing for two field seasons. The last projects to be supported began in 2006 and will conclude early in 2009. In all, more than 100 investigations have been carried out by university researchers, public-agency scientists and private firms since 1997. A total of more than $8 million of Federal and matching funds has been expended on these projects. Typically two to four investigators are involved in each project, and they bring to the project cash or in-kind match of 25 to 150 percent of the amount of the Federal grant. Students are involved in most projects, either as technicians or, more often, as graduate research assistants.

Although not a formal Initiative requirement, publication of research results is strongly encouraged by the Partnership Board and the Steering Committee. More than 40 peer-reviewed publications have been produced to date, along with hundreds of presentations, theses, dissertations and popular articles.

The final Cooperative Agreement between the US Fish & Wildlife Service and the Montana Water Center for the Whirling Disease Initiative was executed in spring 2006, and will terminate in spring 2009. After that time the Initiative website will continue to be maintained by the Water Center, but the site will not be augmented or updated.