Lake Michigan supports an ecosystem that stretches from microscopic bacteria and single-celled algae in the open water column down to mussel beds carpeting the lakebed at depths beyond 80 meters. The lake is home to more than a hundred fish species, dense colonies of invertebrates, seasonal populations of migratory birds, and a microbial community that drives much of the lake’s nutrient cycling. But this ecosystem looks dramatically different today than it did even a few decades ago, reshaped by waves of invasive species, aggressive fishery management, and a changing climate that is altering the lake’s ice cover and wave patterns.
The Invisible Foundation of the Food Web
The base of Lake Michigan’s food web is built by organisms you cannot see without a microscope. Phytoplankton, the tiny photosynthetic organisms suspended in the water column, convert sunlight and dissolved nutrients into the organic matter that feeds everything above them. Among these, diatoms dominate. A study of phytoplankton communities in a Lake Michigan estuary found that diatoms made up over 75% of the community by cell count on the majority of sampling days across all seasons, with especially strong dominance in spring and fall.1Journal of Great Lakes Research. Cold and wet: Diatoms dominate the phytoplankton community during a year of anomalous weather in a Great Lakes estuary Diatoms are glass-shelled algae that thrive in cold, nutrient-rich water, which makes Lake Michigan’s long winters and deep mixing ideal for them.
Below the phytoplankton, the lake’s bacterial communities do the unglamorous work of recycling nutrients and decomposing organic matter. Nearshore bacterioplankton surveys have found that a group called Betaproteobacteria dominates the microbial community, comprising roughly 40 to 68% of sampled bacterial sequences depending on location and season.2PubMed Central. Temporal and spatial variability in nearshore bacterioplankton communities of Lake Michigan These bacteria are widespread in freshwater lakes generally, and their abundance in Lake Michigan’s nearshore zone reflects just how productive those shallow margins are compared to the open lake.
The Deepwater Creatures Most People Never Think About
For decades, the quiet engine of Lake Michigan’s deepwater food web was a tiny shrimp-like crustacean called Diporeia. Smaller than a grain of rice, these amphipods once carpeted the lake bottom in staggering numbers, grazing on the rain of dead phytoplankton that sank from above. They were the critical link between primary production at the surface and the fish that fed in the cold depths. Deepwater sculpin, bloater, lake whitefish, and alewife all depended heavily on Diporeia as a calorie-dense food source.
Then, during the 1990s and 2000s, Diporeia populations collapsed across much of the lake. The crash coincided with the spread of invasive dreissenid mussels, and researchers attributed the decline to mussel effects, though the exact mechanism remained unclear.3Journal of Great Lakes Research. Changes in the Lake Michigan food web following dreissenid mussel invasions: A synthesis The consequences rippled upward through the food web. Alewife, lake whitefish, deepwater sculpin, and bloater all showed reduced body condition, slower growth, or lower energy density as their primary prey vanished.3Journal of Great Lakes Research. Changes in the Lake Michigan food web following dreissenid mussel invasions: A synthesis Research at sites where Diporeia still persisted found that deepwater sculpin had energy densities 31 to 34% higher than sculpin at sites where the amphipod had disappeared.4PubMed. Declines in deepwater sculpin Myoxocephalus thompsonii energy density associated with the disappearance of Diporeia spp. in lakes Huron and Michigan In other words, the fish were not just eating less; they were measurably less nutritious themselves, which matters for every predator above them.
Invasive Mussels and the Reshaping of the Lakebed
The organisms most responsible for remaking Lake Michigan’s ecosystem over the past three decades are quagga mussels. These small bivalves, native to the Ponto-Caspian region of eastern Europe, arrived in ballast water and spread aggressively through the Great Lakes beginning in the 1990s. By recent surveys, they have colonized not just the nearshore zone but deep offshore waters as well, with maximum biomass occurring between 81 and 100 meters of depth. Recruitment continues in the deepest portions of the lake, suggesting the expansion is not finished.5ScienceDirect (Journal of Great Lakes Research). Quagga mussels continue offshore expansion in Lake Michigan, but slow in Lake Huron
What makes quagga mussels so ecologically disruptive is their filter-feeding. Huge populations of mussels strip phytoplankton and other suspended particles from the water, reducing the food available to organisms that once fed on those same particles. The mussels also alter cycles of carbon, nitrogen, and phosphorus through their feeding and waste, changing the distribution and forms of these nutrients across the lake.5ScienceDirect (Journal of Great Lakes Research). Quagga mussels continue offshore expansion in Lake Michigan, but slow in Lake Huron One visible consequence has been the proliferation of Cladophora, a filamentous green alga that now forms thick mats along rocky nearshore stretches. The spread of invasive mussels has altered primary productivity in the nearshore zone, creating conditions that favor these algal blooms.6PubMed Central. Influence of Cladophora-Quagga Mussel Assemblages on Nearshore Methylmercury Production in Lake Michigan When Cladophora detaches and washes ashore, it rots on beaches in foul-smelling heaps, but the ecological impact goes deeper: the algal mats can harbor bacteria and affect mercury cycling in nearshore sediments.
The combined effect of quagga mussel filtration and Diporeia collapse has fundamentally redirected energy flow in the lake. Before the mussels, nutrients cycled through a pelagic food web: phytoplankton to zooplankton to small fish to large fish. Now, a huge fraction of that energy is diverted to the lake bottom, filtered and locked up by mussels. The open-water food web has gotten leaner while the lakebed has gotten richer, a shift researchers sometimes call the “nearshore shunt.”
Lake Trout, Sea Lampreys, and the Fish That Were Stocked to Fill a Gap
Lake Michigan’s fish community tells a story of loss, intervention, and ongoing management. The lake’s original top predator was the lake trout, a cold-water species that once supported a major commercial fishery. By the mid-1950s, lake trout had been exterminated from Lake Michigan, driven to extinction by the combined pressure of intensive commercial fishing and predation by sea lampreys.7Canadian Journal of Fisheries and Aquatic Sciences. Lake Trout (Salvelinus namaycush) and Sea Lamprey (Petromyzon marinus) Populations in Lake Michigan, 1971–78 Sea lampreys, parasitic jawless fish that attach to host fish and drain their blood, had invaded the Great Lakes through shipping canals and devastated native fish populations.
The response came in two parts. First, fisheries managers attacked the lamprey problem directly. Lampricide treatment of Lake Michigan tributaries with a chemical called TFM reduced spawning-phase sea lamprey numbers by about 85%, and the lake’s fishery showed noticeable recovery by the late 1970s.8Journal of Great Lakes Research. A Case History of Sea Lamprey Control in Lake Michigan: 1979 to 1999 TFM works by disrupting the lamprey’s ability to produce cellular energy, draining glycogen stores in the brain and liver until the animal dies from what amounts to an energy crisis, and it is relatively selective for lampreys over most other fish.9PubMed. Failure of ATP supply to match ATP demand: the mechanism of toxicity of the lampricide, 3-trifluoromethyl-4-nitrophenol (TFM), used to control sea lamprey (Petromyzon marinus) populations in the Great Lakes Lamprey control continues today and remains one of the most important ongoing management programs in the Great Lakes.
Second, managers launched a massive stocking program. Lake trout stocking began in 1965 and has continued for decades, though establishing self-sustaining wild populations has proven stubbornly difficult.10Journal of Great Lakes Research. Progress Toward Lake Trout Restoration in Lake Michigan Alongside the native species, managers also introduced Pacific salmon, most prominently Chinook salmon, beginning in the 1960s. The Chinook were brought in partly to control alewife, another invasive fish that had exploded in numbers after the collapse of its native predators. Chinook became the predominant predator on alewives in the lake and the centerpiece of a recreational fishery worth hundreds of millions of dollars annually.
Alewife, Chinook, and the Balancing Act
The relationship between alewife and Chinook salmon defines much of modern Lake Michigan fishery management. Alewife, a small silver herring-like fish native to the Atlantic coast, entered the Great Lakes through canals and proliferated in the absence of top predators. At their peak, massive die-offs of alewife washed up on beaches in windrows, creating public health nuisances. The stocking of Chinook salmon was designed, in part, to eat the alewife problem away.
It worked, perhaps too well. Chinook predation became the primary driver of alewife population trends. When a bacterial kidney disease outbreak weakened the Chinook population in the mid-1980s, the partial relaxation of predation allowed alewife biomass to increase moderately, and it fluctuated around that higher level for more than 15 years.11Canadian Journal of Fisheries and Aquatic Sciences. Response of alewife abundance to the bacterial kidney disease outbreak in the Chinook salmon population of Lake Michigan: importance of predation The episode illustrated how tightly coupled the predator-prey relationship had become. Managers now walk a fine line: stock too many Chinook and the alewife population crashes, potentially starving the salmon; stock too few and alewife rebound to nuisance levels. Modeling work has shown that adjustments like increasing angler bag limits for Chinook would have a relatively minor impact on overall alewife abundance lakewide, which gives managers some room to adjust harvest without destabilizing the forage base.12North American Journal of Fisheries Management. Effects of Increasing Chinook Salmon Bag Limits on Alewife Abundance: Implications for Lake Michigan Management Goals
It is worth pausing to appreciate how artificial this arrangement is. The dominant predator and the dominant prey fish in Lake Michigan are both introduced species. The native lake trout, despite decades of stocking, have not regained a self-sustaining foothold in most of the lake. The ecosystem that anglers and tourists interact with is largely a managed construct layered on top of an invaded system.
Other Fish Worth Knowing About
Beyond the headline species, Lake Michigan supports a range of native and introduced fish. Bloater, a deepwater relative of lake whitefish, persists in cold offshore waters where it feeds on zooplankton and whatever benthic invertebrates remain. Bloaters also serve as hosts for a diverse parasite community, including tapeworms, roundworms, and parasitic copepods, which have been documented at ports around the lake.13Europe PMC. Parasites of Bloater Coregonus hoyi (Salmonidae) from Lake Michigan, U.S.A Parasites are a normal part of any healthy fish community, and their presence in bloater populations tells researchers about food web connections: many fish parasites have complex life cycles that pass through invertebrate hosts before reaching fish.
Cisco, another native cold-water species closely related to lake whitefish, has shown signs of population recovery in recent years. These fish use the drowned river mouth lakes along Lake Michigan’s eastern shoreline as winter foraging habitats. These drowned river mouths are highly productive wetland transitional zones with direct connections to the main lake basin, and they play important seasonal roles for migratory fishes.14ScienceDirect (Journal of Great Lakes Research). Drowned river mouth lakes are winter foraging habitats for the expanding Lake Michigan cisco Coregonus artedi population The fact that cisco are making use of these habitats is an encouraging sign for a species that was once in steep decline.
Yellow perch, walleye, smallmouth bass, and largemouth bass are common in nearshore waters and river connections, sustaining recreational fisheries along the lake’s shores. Invasive round goby, a small bottom-dwelling fish that arrived from the same Ponto-Caspian region as the quagga mussel, has become extremely abundant in nearshore rocky habitats, where it feeds heavily on dreissenid mussels. Goby have become an important prey item for larger fish and diving birds, inserting themselves into the food web as an intermediary between the mussel-dominated benthos and higher predators.
Coastal Habitats and the Nearshore Zone
Lake Michigan’s nearshore zone, from the beach out to roughly 30 meters of depth, is ecologically distinct from the cold, dark offshore. It receives nutrient runoff from land, has warmer summer temperatures, and supports the densest concentrations of submerged aquatic vegetation. USGS surveys using autonomous underwater vehicles have mapped over 300 kilometers of lakebed along the shoreline, documenting the distribution of benthic algae and submerged plants in these shallow areas.15U.S. Geological Survey. Assessment of Submerged Aquatic Vegetation in Lake Michigan Using Down-Looking AUV-Collected Imagery These vegetated areas provide habitat for young fish, invertebrates, and the small organisms that link primary production to the rest of the food web.
The drowned river mouth lakes mentioned earlier are a particularly distinctive feature of Lake Michigan’s eastern coast. Formed when river valleys flooded during post-glacial rebound, these transitional wetlands are common along Michigan’s Lower Peninsula coastline and serve as nurseries and seasonal refuges for multiple fish species.14ScienceDirect (Journal of Great Lakes Research). Drowned river mouth lakes are winter foraging habitats for the expanding Lake Michigan cisco Coregonus artedi population Their direct connections to the main basin make them conduits for nutrients, sediment, and migrating animals.
Beaches, Birds, and Bacteria
Lake Michigan’s sandy beaches are ecosystems in their own right, not the sterile strips of sand they appear to be. Research has shown that beach sand, particularly the wet foreshore zone where waves wash back and forth, harbors persistent populations of E. coli. Studies at a southwestern Lake Michigan beach found that E. coli concentrations were highest in foreshore sand, followed by submerged sediment, and then deeper water. The bacteria recolonized newly placed sand within two weeks, and evidence suggested that E. coli could sustain population density in beach sand during summer without ongoing external inputs from sewage or animal waste.16PubMed Central. Foreshore sand as a source of Escherichia coli in nearshore water of a Lake Michigan beach Wave action then acts as a transport mechanism, washing bacteria from sand into the swimming water and triggering beach advisories even during dry weather.
Gull activity contributes to this cycle. E. coli densities in sand and water were most elevated the day following gull activity in a given area.16PubMed Central. Foreshore sand as a source of Escherichia coli in nearshore water of a Lake Michigan beach Beach management practices matter too: mechanical grooming at a Racine, Wisconsin beach initially increased E. coli in sand, but after adjusting grooming depth and technique, managers achieved a 30% reduction in poor water quality advisories caused by dry weather events.17Aquatic Ecosystem Health & Management. The effect of two mechanical beach grooming strategies on Escherichia coli density in beach sand at a southwestern Lake Michigan beach Heavy rainfall introduces a different source: monitoring at five southern Lake Michigan beaches in 2004 found that sewage was present in a nearby river outfall and on bathing beaches after storms.18PubMed. Nowcast modeling of Escherichia coli concentrations at multiple urban beaches of southern Lake Michigan
Waterbirds themselves face threats tied to the lake’s altered ecology. Outbreaks of avian botulism type E have killed significant numbers of loons, grebes, and other diving birds on Lake Michigan. These die-offs appear linked to the invasive mussel and Cladophora assemblages that now dominate the nearshore benthos: the botulism toxin may accumulate through a chain that runs from bacteria in decaying algal mats, through invertebrates and round goby, to fish-eating birds.
Warming Water and Shrinking Ice
Climate change is adding another layer of disruption. Lake Michigan’s winter ice cover has been declining, and the consequences extend well beyond aesthetics. Reduced ice cover, especially in the northern reaches of the lake, exposes more open water to winter winds, increasing wave height and wave energy during the coldest months. Model simulations project that basin-wide wave heights could increase significantly during winter as regional warming continues and ice cover retreats further.19Frontiers in Marine Science. Wave Climate Associated With Changing Water Level and Ice Cover in Lake Michigan
Larger winter waves mean more coastal erosion, more disturbance to nearshore habitats, and changes to the timing of spring mixing that kicks off the annual plankton bloom. For cold-water species like cisco and lake trout, warming surface temperatures could squeeze suitable habitat into narrower depth bands. For the invasive mussels, warmer conditions and longer ice-free seasons may extend the period over which they can actively filter-feed, potentially intensifying their effects on the plankton community. The lake is not changing in a single direction so much as it is being pulled in several directions at once: warming favors some organisms, stresses others, and creates openings for species nobody has predicted yet.
What Submerged Aquatic Vegetation Tells Us
One of the subtler shifts in Lake Michigan’s ecosystem involves the plants and algae growing on the lakebed. With quagga mussels filtering the water to exceptional clarity in many areas, sunlight now penetrates deeper than it did historically. That has extended the depth range at which photosynthetic organisms can grow on the bottom. In some nearshore areas, beds of native aquatic plants like wild celery and various pondweeds have expanded. In others, the nonnative Cladophora takes advantage of the same clear water and the phosphorus concentrated by mussel waste. The balance between native vegetation recovery and nuisance algal growth varies from site to site and year to year, driven by local substrate, wave exposure, and nutrient inputs. Mapping efforts using underwater vehicles are helping researchers track these changes at scale, covering hundreds of kilometers of lakebed in single survey campaigns.15U.S. Geological Survey. Assessment of Submerged Aquatic Vegetation in Lake Michigan Using Down-Looking AUV-Collected Imagery The results feed into a broader question that Lake Michigan managers are grappling with: is the lake’s increasing clarity a sign of health, or a sign that the food web has been hollowed out by invasive filter-feeders?