Aquatic invasive species have wreaked havoc on the Great Lakes ecosystem. Over 180 non-native species, many of them invasive, have been introduced into the lakes through the Erie and Welland Canals connecting the Great Lakes to the Atlantic Ocean. A current major threat to the lakes is the potential spread of Asian carp into Lake Michigan from the Mississippi River via the Chicago Area Waterway System.

Sea lamprey, alewives, round gobies, zebra mussels, and quagga mussels are a few of the more invasive non-native species that have entered the Great Lakes, decimated populations of native species, and radically altered the ecosystem of the lakes. The ecological and economic damage resulting from these organisms is estimated at over $100 million annually.