For generations, the floodplains and bottomland lakes of the Illinois River in the area of present day Havana supported a rich and diverse community of fish, waterfowl, and other wildlife. Native Americans, explorers, settlers, and sportsmen were drawn to the productivity of Thompson and Flag Lakes. Despite being known as “the most famous and useful breeding ground for the various fish that abound in the Illinois River, and also a wonderful feeding ground for ducks while pursuing their migratory flights…” (Submerged Shore Lands Legislative Investigating Committee, 1911, in Havera et al. 2003), Thompson and Flag Lakes met the same fate as many lakes and floodplains: conversion to farmland.
In the mid-1920’s levees were constructed and the water pumped out of Thompson and Flag Lakes. For nearly 80 years farms existed on what was once a productive aquatic ecosystem. In the early part of the 21st century this began to change. The Nature Conservancy acquired the former sites of Thompson and Flag Lakes, and in 2007, began the process of restoring them to a more natural state.
The restoration has not been without its controversies, but has successfully moved forward and established the Emiquon Preserve, one of the largest undertakings of its kind. In 2012, the Emiquon Complex (consisting of the Emiquon Preserve, Emiquon National Wildlife Refuge, Chautauqua National Wildlife Refuge, and the Illinois State Museum-Dickson Mounds) was recognized as a Wetland of International Importance by the RAMSAR Convention.