Duluth is still an extremely busy shipping port, sending taconite ore and grain east, and receiving products from Europe through the St. Lawrence Seaway. There are over 100 invasive species in the Great Lakes, probably none as damaging as the zebra mussel and sea lamprey. Many of these species came to the lake from ship ballast. All ballast water must be dumped in the Atlantic Ocean before entering the Great Lakes now, but there is still the possibility of new invasive species, so laboratories have been set up to research the problem.
Climate change is already affecting the Apostle Islands, and because of the archipelago's location between biomes (called an ecotone) it may be affected more quickly than many other places. There is also a proposed Concentrated Animal Feeding Operation (CAFO) near the Lakeshore. Warming waters threaten the fish in the lake. Warming air temperatures threaten the boreal forest, and the trees around the lake will probably die out as temperatures rise. As that happens, flora native to Southern Wisconsin will probably move in. It remains to be seen which species will be able to adapt to the rapid change.
The Fond du Lac Dam on the St. Louis River prevents sturgeon from swimming upstream, but there have been recent attempts to improve habitat for them in the estuary below the dam. Wild rice, so important to the region, can only grow in clean water, has been replaced by other grasses. Now that water quality has improved, groups such as the Fond du Lac Band of the Lake Superior Chippewa are attempting to remove the grasses and replant the wild rice. There is also an enormous amount of wood waste from now-closed timber and paper operations that is now being removed. And there's a steel mill superfund site to be cleaned up. There's a long way to go.