Lake Michigan teems with life from its sun-drenched shallows to its cold, dark floor more than 280 meters down. The lake harbors hundreds of species of fish, invertebrates, plankton, birds, and amphibians, but the cast of characters looks nothing like it did a century ago. Invasive species have rewritten the food web so thoroughly that some of the lake’s most iconic fish today, like Chinook salmon, were deliberately introduced by managers, while native creatures that once dominated have been pushed to the margins or wiped out entirely.
The Native Fish That Defined the Lake
For thousands of years, lake trout sat at the top of Lake Michigan’s food chain. These cold-water predators prowled deep reefs and open water, feeding on smaller fish and keeping the ecosystem in balance. By the mid-twentieth century, though, the native lake trout fishery was extinct. Sea lamprey predation, overfishing, and habitat loss combined to eliminate them from the lake, prompting an extensive stocking program of hatchery-reared lake trout beginning in 1965.1Journal of Great Lakes Research. Progress Toward Lake Trout Restoration in Lake Michigan Despite decades of effort, natural reproduction has barely taken hold. Surveys from 1999 to 2001 found that fewer than three percent of spawning lake trout were wild-born fish, and while spawner densities were high enough at certain reef sites for reproduction to occur, something else was preventing young fish from surviving.2North American Journal of Fisheries Management. Relative Abundance, Site Fidelity, and Survival of Adult Lake Trout in Lake Michigan from 1999 to 2001: Implications for Future Restoration Strategies
Deeper in the water column, the bloater remains one of Lake Michigan’s most abundant native fish. Bloaters are members of the whitefish family and serve as a critical forage species, connecting the lower food web to larger predators. They spend their days on or near the bottom and migrate vertically through the water column at night, sometimes traveling through 30 to 65 meters of water to feed on plankton and bottom organisms. Research using acoustics and trawling confirmed that bloaters feed both in the water column and on the bottom, making them opportunistic generalists rather than strictly nocturnal midwater feeders.3Transactions of the American Fisheries Society. Vertical Migration and Nighttime Distribution of Adult Bloaters in Lake Michigan
Lake sturgeon are the lake’s living fossils. These armored, bottom-dwelling fish can grow over two meters long and live past 100 years. They once spawned in many of the rivers that feed Lake Michigan, but dams now block access to the vast majority of suitable spawning habitat. Habitat modeling across five northern Lake Michigan tributaries found that high-quality spawning substrate made up only about one to six percent of available river habitat, and between 30 and 100 percent of it was cut off by dams.4Restoration Ecology. Suitability Modeling of Lake Sturgeon Habitat in Five Northern Lake Michigan Tributaries: Implications for Population Rehabilitation Sturgeon have been documented spawning successfully in the Big Manistee River at water temperatures between roughly 11 and 15°C, but these events are rare and localized.5North American Journal of Fisheries Management. Lake Sturgeon Spawning Habitat in the Big Manistee River, Michigan
Sea Lampreys and the Parasite That Changed Everything
No single creature has reshaped Lake Michigan’s biology more than the sea lamprey. These jawless, eel-shaped parasites entered the Great Lakes through shipping canals in the early twentieth century and found a buffet of fish that had never evolved to survive their attacks. Sea lampreys use suction-cup mouths lined with sharp teeth and a rasping tongue to bore into the sides of host fish, feeding on blood and body fluids. In the Atlantic Ocean, where lamprey and their hosts coevolved, most fish survive. In the Great Lakes, the lamprey are larger and more prolific than native lamprey species, and the hosts simply cannot tolerate them. A single sea lamprey can kill up to roughly 21 kilograms of fish over its parasitic phase.6PubMed Central. Use of physiological knowledge to control the invasive sea lamprey (Petromyzon marinus) in the Laurentian Great Lakes
Control efforts rely heavily on a targeted pesticide called TFM, which is applied to streams where lamprey larvae develop. When combined with a second compound, niclosamide, the concentration of TFM needed to eliminate larvae drops by up to 40 percent, reducing environmental impact on non-target species.7PubMed. Greater than additive interactions between two phenolic pesticides used to control invasive sea lamprey (Petromyzon marinus): Underlying mechanisms and implications Sea lamprey control was one of the prerequisites for the next major chapter in Lake Michigan’s biological story: the introduction of Pacific salmon.
Alewives, Salmon, and a Manufactured Food Chain
Alewives are small, silvery, herring-like fish that invaded the Great Lakes from the Atlantic. By the 1960s they dominated Lake Michigan in staggering numbers, washing up dead on beaches in massive die-offs that fouled the shoreline. Fishery managers decided to stock Pacific salmon, primarily Chinook and coho, both to control the alewife explosion and to create a recreational fishery. The strategy worked on both counts, reducing alewife numbers and generating a sport fishery estimated at around seven billion dollars annually.8Fisheries. Management of Alewife Using Pacific Salmon in the Great Lakes: Whether to Manage for Economics or the Ecosystem?
The catch is that the entire salmon fishery depends on a non-native prey base. As alewife populations have declined under combined salmon predation and ecosystem changes, managers have had to repeatedly cut back salmon stocking to prevent the predator-prey system from collapsing. Analysis has suggested that even after stocking reductions, predatory pressure on alewives remained high, though reductions may have offset the effects of increased natural reproduction by Chinook salmon in tributary rivers.9Transactions of the American Fisheries Society. Changes in the Salmonine Community of Lake Michigan and Their Implications for Predator–Prey Balance Alewives also create a direct problem for native fish recovery: lake trout that eat large amounts of alewife develop a thiamine deficiency because alewives contain an enzyme that destroys thiamine. When alewives make up 35 percent or more of an adult lake trout’s diet, egg thiamine drops enough to cause early mortality syndrome in newly hatched fry.10Journal of Aquatic Animal Health. Development of Thiamine Deficiencies and Early Mortality Syndrome in Lake Trout by Feeding Experimental and Feral Fish Diets Containing Thiaminase This biochemical sabotage is one reason wild lake trout reproduction has stalled despite decades of stocking.
Quagga Mussels and the Reengineered Lakebed
If sea lampreys were the first biological earthquake to hit Lake Michigan, dreissenid mussels were the second. Zebra mussels arrived first, likely in ballast water from ships, but they were eventually eclipsed by their close relative, the quagga mussel. Quagga mussels colonized the entire lakebed, from shallow nearshore zones to the deepest profundal areas. Their collective filter-feeding moved the lake’s biological engine from the open water down to the bottom, a shift researchers describe as moving ecosystem metabolism from water-column dominance to benthic dominance on a basin-wide scale.11PubMed. Ecosystem transformations of the Laurentian Great Lake Michigan by nonindigenous biological invaders
The mussels filter enormous quantities of algae and particulate matter from the water, stripping it of the nutrients and phytoplankton that once fueled the pelagic food web. Seasonal phytoplankton production has plummeted to levels comparable to ultra-clear, nutrient-poor Lake Superior, and the timing of these crashes aligns directly with the expansion of quagga mussel populations.12Environmental Science & Technology. Incidental Oligotrophication of North American Great Lakes One visible consequence: the spread of Cladophora, a filamentous green alga that now carpets rocks and structures in the nearshore zone. With mussels shunting nutrients to the bottom and clearing the water enough for light to reach deeper substrates, Cladophora has proliferated in areas where it was once scarce.13PubMed. Influence of Cladophora-Quagga Mussel Assemblages on Nearshore Methylmercury Production in Lake Michigan
The Collapse of Diporeia and What Replaced It
Diporeia, a tiny shrimp-like amphipod, was once the dominant bottom-dwelling animal in Lake Michigan and a cornerstone of the food web. It fed on the rain of algae that sank from the water column and was in turn eaten by virtually every native fish species that feeds near the bottom. As quagga mussels spread, Diporeia populations crashed. Lake-wide density fell from roughly 5,400 individuals per square meter in the mid-1990s to just 329 per square meter by 2005, and the proportion of sampling sites with no Diporeia at all went from about one percent to nearly 67 percent over the same period.14Freshwater Biology. Transformation of the offshore benthic community in Lake Michigan: recent shift from the native amphipod Diporeia spp. to the invasive mussel Dreissena rostriformis bugensis Surveys in the southern basin showed declines of 89 to 91 percent at shallower sites.15Canadian Journal of Fisheries and Aquatic Sciences. Continued disappearance of the benthic amphipod Diporeia spp. in Lake Michigan: is there evidence for food limitation?
The Diporeia collapse rippled through the food web. Fish that depended on it, including bloaters, sculpins, and whitefish, lost a primary food source. Into the vacuum stepped the round goby, another invasive species from Eurasia that entered the Great Lakes through ballast water. Round gobies are aggressive, bottom-dwelling fish that eat dreissenid mussels, snails, and invertebrates. They have become one of the most abundant fish in nearshore Lake Michigan and now serve as prey for larger predators like smallmouth bass and lake trout, creating a new but ecologically fragile link in the food chain.
The Planktonic Food Web
The open-water food web has been just as thoroughly rearranged. When the spiny water flea, Bythotrephes, invaded Lake Michigan in the 1980s, it hammered native zooplankton. A native predatory cladoceran called Leptodora declined sharply, and the offshore Daphnia community, which had consisted of three species, contracted to dominance by a single one.16Limnology and Oceanography. Food‐web responses to species invasion by a predatory invertebrate: Bythotrephes in Lake Michigan The effects compounded over time: by 2007 and 2008, key herbivorous zooplankton like Daphnia and the copepod Diacyclops declined further, likely from a combination of food limitation driven by mussel filtering and increased predation as Bythotrephes populations grew. The spiny water flea itself benefited from fewer young alewife eating it and from clearer water that improved its hunting efficiency.17Journal of Great Lakes Research. Seasonal zooplankton dynamics in Lake Michigan: Disentangling impacts of resource limitation, ecosystem engineering, and predation during a critical ecosystem transition
The opossum shrimp, Mysis diluviana, is another important member of the deep-water community. These centimeter-long crustaceans undertake daily vertical migrations, rising from deep water toward the surface at night to feed, then returning to depth during the day. They serve as food for fish like bloaters and juvenile lake trout and connect the deep benthic zone to the mid-water food web.
The Invisible Majority
Most of Lake Michigan’s animal life is invisible to anyone standing on a pier. Surveys of the meiobenthos, the tiny animals living in and on the sediment, found total densities ranging from about 70,000 to 1.3 million individuals per square meter. Nematodes accounted for roughly 80 percent of all individuals. Other groups included harpacticoid copepods, tardigrades (the famously indestructible “water bears”), ostracods, rotifers, and tiny cladocerans. Deeper sites tended to harbor more harpacticoids and tardigrades, while cyclopoid copepods and cladocerans were more common in shallower areas.18Journal of Great Lakes Research. Abundance and Biomass of the Meiobenthos in Nearshore Lake Michigan with Comparisons to the Macrobenthos These organisms cycle nutrients through the sediment and serve as food for larger invertebrates and small fish. Sampling methods matter here: standard mesh screens miss a large fraction of these tiny animals, meaning their true abundance is almost certainly higher than published estimates suggest.19Canadian Journal of Fisheries and Aquatic Sciences. Screen Mesh Size Affects Estimates of Macro- and Meio-benthos Abundance and Biomass in the Great Lakes
Birds, Mammals, and Amphibians
Lake Michigan is a major flyway and wintering ground for waterbirds. Loons, mergansers, long-tailed ducks, and grebes are common on the open lake, especially during migration and winter. Gulls and terns patrol the nearshore and nest on islands. In recent years, waterbird die-offs from avian botulism type E have become a recurring concern. Research into the gut contents of Lake Michigan waterbirds identified multiple pathways for the botulism toxin: mollusk-eating birds can pick up the toxin directly from infected dreissenid mussels, while fish-eating birds are exposed through a chain that runs from mussels to round gobies and then to the birds themselves.20Journal of Great Lakes Research. Gut content analysis of Lake Michigan waterbirds in years with avian botulism type E mortality, 2010–2012 Invasive mussels and gobies, in other words, are not just reshaping the underwater food web; they are creating new disease pathways for animals that spend most of their time above the surface.
Along the shoreline and in tributaries, North American river otters have been recolonizing areas where they were once extirpated. These playful, semi-aquatic mammals eat fish, crayfish, and other aquatic prey and are considered indicators of good water quality. Mudpuppies, large fully aquatic salamanders, also inhabit the tributaries and nearshore rocky areas of Lake Michigan. They are nocturnal, preferring cooler water and rocky cover, and are one of the few amphibians that live their entire lives underwater, breathing through feathery external gills. Snapping turtles, painted turtles, and northern water snakes round out the reptile and amphibian community in coastal wetlands and river mouths.
Diseases Lurking in the Water
Fish in Lake Michigan face threats beyond predation and habitat loss. Viral hemorrhagic septicemia virus (VHSV), a pathogen that emerged in the Great Lakes in the mid-2000s, infects a wide range of ecologically and recreationally important species, including muskellunge, bluegill, yellow perch, and freshwater drum.21PubMed Central. Spread of the Emerging Viral Hemorrhagic Septicemia Virus Strain, Genotype IVb, in Michigan, USA Sampling efforts found the virus in multiple species at sites across the Great Lakes, with round gobies and yellow perch among the most frequently infected. Viral loads in positive fish varied enormously, from minimal to millions of gene copies per individual.22PLOS ONE. Distribution of an Invasive Aquatic Pathogen (Viral Hemorrhagic Septicemia Virus) in the Great Lakes and Its Relationship to Shipping Large-scale die-offs have been documented in several Great Lakes, and the virus is thought to have been introduced through ballast water, the same vector responsible for mussels and gobies.
The Asian Carp Question
Bighead and silver carp, collectively called Asian carp, are the most-discussed potential invader. These massive filter-feeding fish have been working their way up the Mississippi River basin toward the Great Lakes for years, prompting the construction of electric barriers in the Chicago Sanitary and Ship Canal. Bioenergetic modeling suggests the open waters of Lake Michigan would be inhospitable to carp because plankton levels are too low to sustain them in most areas. But productive embayments and wetlands are a different story: positive growth was predicted in those habitats, and the models estimated carp could travel more than a kilometer per day without losing body mass in some of those environments.23Freshwater Biology. Can filter‐feeding Asian carp invade the Laurentian Great Lakes? A bioenergetic modelling exercise
Ironically, the very mussels that have devastated the native food web may have made the lake less inviting for carp. The quagga mussel takeover stripped so much plankton from the water that nearshore zooplankton biomass has dropped substantially, and predicted carp growth rates came back negative across most locations sampled. The exceptions were drowned river-mouth lakes along the Michigan coast and parts of Green Bay, Wisconsin, where primary production remains high enough to support filter feeders.24University of Illinois Urbana-Champaign IDEALS. Nearshore zooplankton communities of Lake Michigan and implications for invasibility by Asian carp The concern is that carp could establish footholds in those productive pockets and then move through connected waterways.
Coastal Wetlands as Hidden Nurseries
The drowned river mouths, marshes, and coastal wetlands ringing Lake Michigan are often overlooked, but they play an outsized role in sustaining the lake’s fish community. These shallow, vegetated habitats serve as nurseries for young fish and feeding grounds for adults. Stable isotope analysis of fish captured in both wetland and nearshore habitats showed that a substantial fraction of their nutrition, often more than 30 percent, came from whichever habitat they were not caught in. Fish captured in nearshore areas were getting meaningful energy from wetland food webs, and vice versa.25PubMed Central. Relative contributions of nearshore and wetland habitats to coastal food webs in the Great Lakes Wetlands are not simply exporting energy into the lake; the exchange runs in both directions, with nearshore resources subsidizing wetland food webs as well. This reciprocity means that protecting one habitat without the other leaves the whole system vulnerable. Development, agriculture, and hardened shorelines that disconnect wetlands from the lake can quietly erode the base of the food web that supports everything from yellow perch to herons.
The creatures of Lake Michigan tell a story of ecological upheaval layered on top of deep evolutionary history. Lake sturgeon that outlived the glaciers now bump up against concrete dams. Bloaters still migrate through the water column at night, but the food waiting for them has changed. Salmon draw anglers from across the country, yet they exist only because managers chose to replace one invasive fish with a stocked predator. Even the lakebed sediment, packed with millions of nematodes and tardigrades per square meter, is being reworked by quagga mussels that arrived uninvited a few decades ago. Understanding what lives in Lake Michigan today means understanding that the lake is not a museum exhibit frozen in time but a constantly shifting ecosystem where native holdouts, deliberate introductions, and accidental invasions collide.