Lake Superior holds roughly 80 fish species, making it one of the most diverse coldwater lakes on the continent. The community is built around lake trout as the top predator, with a supporting cast of native prey fish like cisco and lake whitefish, bottom-dwellers such as sculpins, and a handful of introduced species including Chinook and coho salmon. What makes Superior’s fish community unusual among the Great Lakes is how much of it is still native. Decades of sea lamprey control and careful fisheries management have left the lake with a more intact food web than any of its neighbors, though that stability has limits worth understanding.
Lake Trout and Their Remarkable Variety
Lake trout are the keystone species in Lake Superior, and they come in more forms here than anywhere else. Researchers recognize at least four distinct morphs: leans, siscowets, humpers, and redfins. Leans are the classic lake trout most anglers encounter, living in nearshore waters down to moderate depths. Siscowets are the deep-water version, extremely fat-bodied fish that can live at depths exceeding 300 meters. Humpers tend to occupy isolated offshore reefs, and redfins are found in deep offshore habitats. A large sampling effort across six locations in the lake documented all four morphs, with siscowets being the most numerous in the catches, followed by leans, humpers, and redfins.1Journal of Great Lakes Research. Life-history variation among four lake trout (Salvelinus namaycush) morphs at six locations in Lake Superior
These aren’t just cosmetic differences. Genetic work has found evidence of divergent selection between the ecotypes, with differentiated gene regions linked to relevant biological functions like depth preference and fat metabolism. The researchers describe it as a “continuum of divergence,” meaning the four morphs aren’t cleanly separated species but represent an ongoing evolutionary process where a single ancestral population is splitting into specialized forms.2PubMed. Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior For the lake’s ecology, the practical upshot is that lake trout collectively occupy almost every depth zone. Lean lake trout dominate nearshore waters as the most abundant predator, while siscowets rule the offshore deep.3Journal of Great Lakes Research. Lake Superior fish community and fisheries, 2001–2022: An era of stability
The Native Prey Fish
Cisco, also called lake herring, is the most important native forage fish in the system. During the first half of the twentieth century, cisco populations were enormous and supported massive commercial fisheries across the Great Lakes. Most of those populations collapsed by 1970, but Lake Superior’s cisco have staged a meaningful recovery since then, something no other Great Lake can claim.4North American Journal of Fisheries Management. A Synthesis of Cisco Recovery in Lake Superior: Implications for Native Fish Rehabilitation in the Laurentian Great Lakes That said, contemporary abundance is still considered below historical levels, and recruitment has been intermittent rather than steady year after year.5Fisheries Management and Ecology. Was historical cisco Coregonus artedi yield consistent with contemporary recruitment and abundance in Lake Superior?
Lake whitefish are another pillar of the native community and still support a commercial fishery, particularly in Canadian waters. They’re bottom-feeders in shallower zones, filling a different niche than the mid-water cisco. Both species have benefited from lake trout refuges in the Apostle Islands region, where fishing restrictions have helped populations grow. During a nearly three-decade monitoring period, lake whitefish abundance increased faster inside the refuges than outside them.6ScienceDirect (Journal of Great Lakes Research). Effects of lake trout refuges on lake whitefish and cisco in the Apostle Islands Region of Lake Superior
Rounding out the native prey base are bloaters and kiyi, two deepwater cisco species, along with various sculpin species. The opossum shrimp Mysis and the amphipod Diporeia are invertebrates rather than fish, but they’re so central to the food web that they deserve mention. Recent food-web studies found that planktivorous and bottom-feeding fish rely heavily on Mysis, with less dependence on Diporeia than in the past.7Journal of Great Lakes Research. Food web structure of the Lake Superior fish community in 2021–2022 Rainbow smelt, a non-native forage fish, also plays a significant role in sustaining predators, particularly Pacific salmon. The interplay between native and non-native prey fish is one of the more dynamic parts of the food web.8Ecosystems. Sustainability of the Lake Superior Fish Community: Interactions in a Food Web Context
Other Native Species Worth Knowing
Brook trout are one of only two salmonid species actually native to Lake Superior (the other being lake trout). They’re mostly a nearshore and tributary fish. A tracking study in Nipigon Bay found that brook trout stayed almost exclusively in shallow water, with the vast majority of detections at less than seven meters deep and within 400 meters of shore. They moved to slightly deeper areas in midsummer when shallow water got too warm, then ascended tributaries to spawn in early October before returning to the lake.9Taylor & Francis Online / Transactions of the American Fisheries Society. Habitat Use and Movement Patterns of Brook Trout in Nipigon Bay, Lake Superior Rehabilitating brook trout populations is now a management priority after decades of focus on lake trout.3Journal of Great Lakes Research. Lake Superior fish community and fisheries, 2001–2022: An era of stability
Lake sturgeon are the ancient giants of the system, with individuals that can exceed a hundred pounds and live for decades. They spawn in tributaries, and dams have been a persistent barrier to their migrations. In the Black Sturgeon River, for instance, nearly all sturgeon that entered the river migrated to the base of the dam, unable to pass it.10Ecology of Freshwater Fish. The spatial extent of Walleye and Lake Sturgeon spawning migrations below a dam in the lower Black Sturgeon River, Lake Superior Reintroduction efforts have shown promise in some watersheds, particularly in the St. Louis River estuary, where improved water quality and relatively intact spawning habitat have helped. Stocked juvenile sturgeon stayed in the estuary for up to five years before venturing into Lake Superior proper.11North American Journal of Fisheries Management. Reintroduction of Lake Sturgeon in the St. Louis River, Western Lake Superior
Walleye are present in Lake Superior, concentrated mainly in warmer bays and river mouths. They’re not nearly as dominant as in shallower, warmer lakes, but they’re a valued sport fish where they occur, and their rehabilitation is part of the current management agenda. Yellow perch, northern pike, and burbot also inhabit the lake, mostly in nearshore and bay environments where conditions are more hospitable than the open, cold, deep waters that define most of Superior’s vast area.
Muskellunge are a more surprising resident. Acoustic tracking of 60 adult muskellunge in the St. Louis River estuary and southwestern Lake Superior revealed that these fish do use the open lake itself, not just the sheltered estuary. Interestingly, the Minnesota genetic strain made up about 80 percent of the individuals detected using Lake Superior, compared to the Wisconsin strain, suggesting strain-level behavioral differences in how willing these fish are to venture into open water.12Oxford Academic. Muskellunge Spatial Ecology in the St. Louis River Estuary and Southwestern Lake Superior
The Sea Lamprey Problem and How It Reshaped the Lake
No discussion of Lake Superior’s fish makes sense without understanding what sea lampreys did to the system. These parasitic, eel-shaped invaders entered the upper Great Lakes in the late 1930s and began devastating fish stocks by the mid-1950s in Superior.13Canadian Journal of Fisheries and Aquatic Sciences. Sea Lamprey (Petromyzon marinus) in Lakes Huron, Michigan, and Superior: History of Invasion and Control, 1936–78 Lake trout populations crashed. The commercial fishery that depended on them cratered. Combined with overfishing that was already under way, the collapse was severe enough that it restructured the entire food web.
Control efforts eventually turned the tide. Starting in 1958, a selective chemical called TFM was applied to streams where lamprey larvae develop. Mechanical and electrical barriers were installed to block spawning runs. By 1996, self-sustaining lake trout populations had been restored across most of the lake. But “restored” doesn’t mean lamprey-free. Sea lamprey abundance declined steadily over decades, yet it never fell as low as the targets that managers set. Most of the parasitic lampreys that remain in the lake probably originate from larvae that survive chemical treatments, and they still kill lake trout every year.14Journal of Great Lakes Research. Sea Lamprey Abundance and Management in Lake Superior, 1957 to 1999
The recovery of lake trout after lamprey suppression set off a cascade of changes in how species interacted. Time-series analysis of commercial fish catches showed that relationships between species shifted after lamprey control took hold, affecting not just lake trout but also whitefish, cisco, walleye, and yellow perch.15Canadian Journal of Fisheries and Aquatic Sciences. Changes in Species Interactions of the Lake Superior Fisheries System After the Control of Sea Lamprey as Indicated by Time Series Models The food web today is largely a product of this recovery process.
Introduced Salmon and the Sport Fishery
Chinook salmon and coho salmon are not native to Lake Superior. They were stocked beginning in the 1960s and 1970s to create a sport fishery and to control invasive alewife and smelt populations. Chinook became the glamour fish for trolling anglers, and for a while stocking was heavy. In the 1990s, hatchery fish made up varying proportions of the Chinook population depending on jurisdiction: around 9 percent in Ontario waters, 25 percent in Michigan, 32 percent in Wisconsin, and 57 percent in Minnesota. In tributaries where stocking occurred, hatchery fish dominated spawning runs, but in unstocked streams most Chinook were wild-born, indicating successful natural reproduction.16Taylor & Francis Online. Contribution of Hatchery-Reared Fish to Chinook Salmon Populations and Sport Fisheries in Lake Superior
Management philosophy has shifted considerably since then. Stocking of non-native salmon was reduced by about 74 percent as lake trout populations recovered and the emphasis moved toward native species.17Journal of Great Lakes Research. Lake Superior fish community and fisheries, 2001–2022: An era of stability Chinook and coho now sustain themselves largely through natural reproduction rather than hatchery input, making the lake somewhat unusual among Great Lakes sport fisheries. Steelhead (the migratory form of rainbow trout) and pink salmon, another Pacific species, are also present, the latter having established self-reproducing populations after accidental introductions decades ago.
The Deep, Dark, and Rare
Lake Superior’s deepwater zone, which can exceed 400 meters, hosts some genuinely unusual fish. The deepwater sculpin lives on the bottom in these cold, lightless environments and has evolved extraordinary visual sensitivity. Experiments showed that this species needed more than three minutes of dark adaptation between light flashes to fully recover its visual response, suggesting it may be the most light-sensitive of the deepwater fish tested. That sensitivity allows it to detect predators and prey in the near-total darkness of the lake floor.18PLoS ONE. Visual Sensitivity of Deepwater Fishes in Lake Superior
Among the rarer inhabitants is the shortjaw cisco, a deepwater coregonid that was once the most abundant deepwater cisco in Lake Superior in the early 1920s. It has declined so severely that it now makes up less than one percent of all deepwater ciscoes captured in surveys. Population modeling suggests that quasi-extinction is a real possibility in the near future.19Transactions of the American Fisheries Society. Decline of shortjaw cisco in Lake Superior: the role of overfishing and risk of extinction The kiyi, another deepwater cisco, is in somewhat better shape and remains an important part of the deepwater food web, but the overall pattern for the lake’s deepwater specialists has been one of decline from historical levels.
How Warming Water Is Rearranging the Map
Lake Superior is warming, and that is already changing which fish can live where. Modeling work covering 1979 to 2006 found that the number of days with suitable thermal habitat increased by about six days per decade for lean lake trout, seven for Chinook salmon, and five for walleye. For all three species, the spatial extent of preferred-temperature water also grew substantially each year. The losers in this equation are the coldest-water fish. Siscowet lake trout, which prefer the chilliest depths, lost about three days of preferred habitat per decade and saw their suitable area shrink by roughly 161 square kilometers per year during the same period.20PLoS ONE. Climate Change Expands the Spatial Extent and Duration of Preferred Thermal Habitat for Lake Superior Fishes
Greater habitat overlap among species that historically stayed in separate thermal zones could intensify competition for food. And continued warming may make conditions more hospitable for invasive species that have struggled in Superior’s cold water, potentially undermining the stability that has defined the lake’s fish community for the past two decades.
Mercury and What It Means for Eating Lake Superior Fish
Lake Superior fish are generally safe to eat, but they do carry measurable levels of mercury and PCBs, which accumulate in larger, longer-lived predators. Tribal fish harvests from the upper Great Lakes have been monitored for these contaminants, and the levels still require careful guidance for consumers, particularly for vulnerable groups like pregnant women and children.21PubMed Central. Mercury, Polychlorinated Biphenyls, Selenium, and Fatty Acids in Tribal Fish Harvests of the Upper Great Lakes
Mercury levels vary dramatically by lake trout ecotype. A recent study found that redfins had the highest average mercury concentrations, followed by siscowets, humpers, and leans. The lean lake trout that most anglers catch and eat had the lowest levels among the four morphs. The differences appear to be driven by diet and growth efficiency: ecotypes that eat more insects tend to have lower mercury burdens than those relying more heavily on fish prey at depth.22PubMed. Trophic ecology and mercury bioaccumulation among Lake Superior lake charr (Salvelinus namaycush) ecotypes For anyone eating their catch, the practical takeaway is that smaller lean lake trout are the safest choice among the lake trout family, while the deep-dwelling morphs carry a higher contaminant load. State and provincial consumption advisories provide specific meal-frequency recommendations that reflect these differences.
Why Superior’s Fish Community Stands Apart
Compared to the other Great Lakes, Lake Superior’s fish community is unusually native-dominated. Lakes Michigan, Huron, and Ontario saw their native food webs largely replaced by invasive species like alewife, round goby, and quagga mussels, all of which are absent or far less established in Superior. The cold temperatures, low nutrient levels, and relatively intact predator-prey relationships have created what researchers describe as ecological redundancies, meaning multiple native species fill overlapping roles, so the food web doesn’t hinge on any single species to function.3Journal of Great Lakes Research. Lake Superior fish community and fisheries, 2001–2022: An era of stability Rainbow smelt is the main exception, a non-native prey fish that has embedded itself in the food web so thoroughly that Pacific salmon and some native predators depend on it.8Ecosystems. Sustainability of the Lake Superior Fish Community: Interactions in a Food Web Context
The period from 2001 to 2022 has been characterized as an era of stability for the lake’s fish community, with recreational fishery yields holding steady even as non-native salmon stocking was dramatically reduced. That stability isn’t guaranteed forever, but for now, Lake Superior remains the closest thing to a functioning pre-colonial Great Lakes fish community that still exists.