The Winnebago Lakes Council is a non-profit organization focused on charitable, educational, and scientific purposes. The organization is governed by a Board of Directors elected by dues-paying members. Membership is open to anyone who subscribes to its mission. Funding comes from dues, donations, and grants.

The Winnebago Lakes system is the largest inland water body in Wisconsin. It is a highly productive warm water fishery, the state's most popular inland boating destination, and provides drinking water for most people in surrounding counties.

Conflicting uses and increased development pressures make it challenging to manage. Over the past century, ecosystems have steadily deteriorated, despite protective efforts by state and federal agencies, local government, and citizens' groups. Phosphorus pollution, loss of wildlife habitat, exotic species, and shoreline erosion are major issues. A strong, unified voice of concerned users and residents increases the likelihood that a system of this size can reach its environmental quality goals.