Lake Ontario holds a mix of roughly 130 fish species, but the roster looks nothing like what swam here two centuries ago. A handful of native predators that once dominated the lake, including lake trout, Atlantic salmon, and deepwater ciscoes, were driven to the brink or eliminated entirely by the mid-twentieth century. Their ecological roles have been partially filled by intentionally stocked Pacific salmon, while uninvited arrivals like sea lampreys, alewives, and round gobies have reshaped the food web from the bottom up. Understanding which fish are native, which were introduced on purpose, and which crashed the party on their own is the key to making sense of this lake’s strange, constantly shifting ecology.
The Native Predators That Were Lost
Lake Ontario’s original apex fish were lake trout and Atlantic salmon. Both species were commercially and recreationally important for centuries, but by the mid-1900s neither could sustain itself. Lake trout were essentially gone from the lake by around 1950, wiped out by a combination of overfishing, habitat degradation, and parasitism by invasive sea lampreys.1CrossRef. Population Dynamics of Lake Ontario Lake Trout during 1985–2007 Atlantic salmon disappeared even earlier. Commercial catch records show that Atlantic salmon, lake trout, burbot, deepwater ciscoes, and lake whitefish all vanished or declined severely over the same general period.2CrossRef (Journal of the Fisheries Research Board of Canada). Lake Ontario: Effects of Exploitation, Introductions, and Eutrophication on the Salmonid Community
Restoration efforts for lake trout began in the 1970s through stocking programs, sea lamprey control, and harvest restrictions. A stocking-supported population now exists, but natural reproduction remains stubbornly limited. Surveys from 1985 through 2007 showed lake trout abundance actually dropped by about 76%, even though stocking levels stayed relatively flat. The main culprit appeared to be a sharp rise in natural mortality among young fish.1CrossRef. Population Dynamics of Lake Ontario Lake Trout during 1985–2007 One reason for that high early mortality: invasive alewives eat lake trout fry. Researchers examining alewife stomachs near spawning reefs found lake trout fry inside almost 10% of the alewives caught, a discovery that suggested alewife predation could be a major bottleneck preventing natural lake trout recovery.3ScienceDirect. Predation by Alewives on Lake Trout Fry in Lake Ontario: Role of an Exotic Species in Preventing Restoration of a Native Species
Atlantic salmon reintroduction has followed a parallel but equally difficult path. Hatchery-reared smolts are stocked into tributaries to supplement what little natural spawning occurs. Research using acoustic telemetry found that while hatchery and naturally reared smolts migrate similarly, hatchery fish survive at lower rates, a gap that complicates efforts to rebuild a self-sustaining run.4CrossRef. Survival and migration patterns of naturally and hatchery‐reared Atlantic salmon (Salmo salar) smolts in a Lake Ontario tributary using acoustic telemetry Decades of work have not yet produced either a self-sustaining lake trout population or a viable Atlantic salmon fishery in the lake, though biologists continue to refine stocking strategies.
Deepwater Natives and the Bloater Comeback Attempt
Below the sunlit surface waters, Lake Ontario once supported a community of deepwater ciscoes, sometimes called chubs. Among these, the bloater was a key planktivore, feeding on tiny organisms in the deep, cold layers of the lake. Commercial fishery records suggest bloaters were common through the early 1900s, but by the 1950s they had vanished from catches. Decades of annual trawl surveys beginning in 1978 turned up exactly one individual, in 1983.5ScienceDirect. Results of the collaborative Lake Ontario bloater restoration stocking and assessment, 2012–2020
In 2012, a multiagency program began stocking bloaters into Lake Ontario using eggs collected from Lake Michigan populations. Over the next eight years, more than a million fish were released. The results so far have been modest: bottom trawl surveys detected stocked bloaters starting in 2015, but through 2020 only ten individuals had been recaptured.5ScienceDirect. Results of the collaborative Lake Ontario bloater restoration stocking and assessment, 2012–2020 A million fish in, ten fish recaptured. That ratio gives you a sense of how difficult it is to reestablish a deepwater species once it has been functionally lost from a lake system. Whether those stocked bloaters can eventually find each other, spawn, and build a population remains an open question.
Warmwater Natives Along the Shore
Not every native fish story in Lake Ontario is grim. The lake’s nearshore zone supports a community of warmwater species including largemouth and smallmouth bass, yellow perch, pumpkinseed sunfish, northern pike, and bowfin, among others. Two decades of monitoring along the Toronto waterfront found that native warmwater species have become more dominant in recent years, suggesting that habitat restoration work in urban shoreline areas is paying off.6PLoS One. Nearshore fish community changes along the Toronto waterfront in accordance with management and restoration goals: Insights from two decades of monitoring Wetland rehabilitation, improved water quality, and shoreline naturalization have given these species more usable habitat.
Warmwater natives also tend to be more resilient to some of the pressures that gutted coldwater populations. They are less vulnerable to sea lamprey attack, less dependent on the open-water prey base that alewives disrupted, and better adapted to the increasingly warm conditions the lake is experiencing. For recreational anglers, these species provide reliable fishing close to shore, especially in bays, harbors, and river mouths.
Pacific Salmon and the Intentional Stocking Era
With native predators gone, fishery managers in the late 1960s made a deliberate choice to stock Pacific salmon, primarily Chinook salmon, into Lake Ontario. The goal was practical: control the exploding alewife population while creating a sport fishery. That decision transformed the lake. Chinook became the backbone of a recreational fishery worth hundreds of millions of dollars annually across the Great Lakes.
What surprised managers was how well Chinook reproduced on their own. Analysis of scale patterns in age-3 Chinook salmon from 1992 to 2005 showed that, on average, about 62% were wild-born rather than hatchery-stocked.7ScienceDirect (Journal of Great Lakes Research). Majority of age-3 Chinook salmon (Oncorhynchus tshawytscha) in Lake Ontario were wild from 1992 to 2005, based on scale pattern analysis That proportion fluctuated between roughly a quarter and over 80% depending on the year, but the takeaway is clear: Chinook have established natural reproduction in Lake Ontario’s tributaries to a degree their native predecessors have not managed since restoration began.
During the period from 1989 to 2005, the lake supported an average alewife biomass of about 174,000 metric tons. Chinook salmon of ages one through four consumed an estimated 22% of that alewife biomass each year on average, with some years reaching over 40%.8CrossRef. Lakewide Estimates of Alewife Biomass and Chinook Salmon Abundance and Consumption in Lake Ontario, 1989–2005: Implications for Prey Fish Sustainability Since Chinook are only one of several stocked salmonids eating alewives (coho salmon, steelhead rainbow trout, and brown trout also depend on them), total predation pressure raises real questions about whether the alewife population can sustain this demand long-term. Managers walk a tightrope: stock enough predators to control alewives but not so many that the prey base collapses and takes the fishery with it.
Sea Lampreys and the Fight to Control Them
Sea lampreys are arguably the most destructive invasive fish in the Great Lakes. These jawless, parasitic animals attach to host fish and feed on their blood and body fluids, frequently killing larger fish like lake trout and salmon. They played a central role in the collapse of Lake Ontario’s native predator populations.
The primary weapon against sea lampreys has been the chemical lampricide TFM (3-trifluoromethyl-4-nitrophenol), applied to tributaries where lamprey larvae develop. Treatments of Lake Ontario tributaries began in 1971, with expanded treatments of Oneida Lake and Lake Erie tributaries following in the 1980s. The program worked: by the mid-1980s through early 1990s, anglers in U.S. waters of Lake Ontario were harvesting about 2.4 times as many lake trout as sea lampreys were killing, a reversal of the earlier dynamic where lampreys overwhelmed hatchery fish before they could mature.9U.S. Geological Survey. Lake trout rehabilitation in Lake Ontario
TFM is effective against lamprey larvae, but it is not perfectly selective. Research on juvenile lake sturgeon, a threatened native species whose habitat overlaps with lamprey nursery areas, found that environmentally relevant concentrations of TFM cause serious metabolic disruption. Exposure reduced brain energy stores by 50 to 60% and liver glycogen by more than 50%, leading to impaired performance and, in some cases, death.10Oxford Academic. The lampricide 3-trifluoromethyl-4-nitrophenol causes temporary metabolic disturbances in juvenile lake sturgeon (Acipenser fulvescens): implications for sea lamprey control and fish conservation Managers now consider timing treatments to avoid peak sturgeon vulnerability, such as delaying applications to late summer or fall. The tension between controlling one invasive species and protecting a threatened native one is a recurring theme in Great Lakes management.
Alewives and What They Changed
Alewives, a small herring native to the Atlantic coast, entered Lake Ontario and eventually became the dominant forage fish. Their sheer abundance restructured the food web. They outcompeted native prey fish for zooplankton, they preyed on the eggs and fry of species managers were trying to restore, and their population swings caused massive die-offs that fouled beaches. The discovery of lake trout fry inside alewife stomachs near known spawning reefs pointed to a direct mechanism by which alewives suppress native predator recovery.3ScienceDirect. Predation by Alewives on Lake Trout Fry in Lake Ontario: Role of an Exotic Species in Preventing Restoration of a Native Species
At the same time, alewives became the foundation of the stocked salmon fishery. Without a large alewife population, Chinook and coho salmon have nothing to eat. This creates an uncomfortable dependency: the entire recreational salmonid fishery rests on the continued presence of an invasive species that also happens to be one of the biggest obstacles to restoring native fish. It is an ecological contradiction that managers have been navigating for decades, and there is no clean resolution in sight.
Round Gobies and the Reshaping of the Bottom
Round gobies arrived in the Great Lakes in ballast water from the Black and Caspian Sea regions and were first documented in Lake Ontario’s Hamilton Harbour, where researchers later analyzed data from the spread phase of the invasion.11Europe PMC. Invasion dynamics of round goby (Neogobius melanostomus) in Hamilton Harbour, Lake Ontario These small, aggressive bottom-dwellers eat the eggs of native fish, compete with native sculpins and darters for food and shelter, and devour invertebrates at rates that visibly alter the bottom community.
Studies in the upper St. Lawrence River, which connects to Lake Ontario, found that macroinvertebrate diversity declined with increasing goby density. The biomass of non-mussel invertebrates was negatively correlated with goby numbers, with snails (gastropods) hit especially hard. An unexpected secondary effect: as gobies reduced gastropod populations, algae that those snails would have grazed grew thicker, creating a trophic cascade visible on the rocks.12CrossRef. Impacts of the Eurasian round goby (Neogobius melanostomus) on benthic communities in the upper St. Lawrence River Even at sites where gobies had been established for 17 to 19 years, their negative impact on invertebrate diversity persisted, suggesting this is not a temporary disruption but a permanent restructuring of the bottom community.13ScienceDirect. Two decades since first invasion: Revisiting round goby impacts on nearshore aquatic communities in the Upper St. Lawrence River
On the other hand, round gobies have become a significant food source for larger fish, including smallmouth bass and lake trout. Some anglers and biologists view them as an established, if unwanted, component of the food web that now provides calories to species people care about. Their role is complicated rather than purely negative.
Zebra and Quagga Mussels as Ecosystem Engineers
While not fish themselves, invasive dreissenid mussels (zebra mussels and, increasingly, quagga mussels) have fundamentally altered the conditions in which Lake Ontario’s fish live. Their filter-feeding clears the water dramatically, stripping out phytoplankton and redirecting nutrients like phosphorus away from the open-water food web. This increased water clarity sounds like a good thing, but it starves the base of the pelagic food chain, reducing the zooplankton that small fish depend on. The mussel invasion has also been associated with conditions that favor toxic cyanobacteria blooms by changing nutrient ratios and allowing more light into the water.14ScienceDirect. The Great Lakes’ most unwanted: Characterizing the impacts of the top ten Great Lakes aquatic invasive species
For fish, the practical result is that energy that used to flow through open-water plankton now gets diverted to the near-bottom mussel beds, a process sometimes called the “nearshore shunt.” Species that can exploit nearshore and benthic food sources, like round gobies, benefit. Species that depend on open-water plankton chains, like the alewives that salmon eat, face a less productive environment. The mussels are, in effect, rewiring the lake’s energy budget.
The Spiny Water Flea and Contaminant Surprises
Another invertebrate invader worth mentioning is the spiny water flea (Bythotrephes), a tiny predatory crustacean that alters the zooplankton community fish rely on. Its impact on fish is not always straightforward. Research on cisco, a native coldwater species present in some Great Lakes waters, found that after spiny water flea invasion, cisco actually grew faster and accumulated less mercury per unit of trophic position. The likely explanation is that changes in the prey community improved the energy efficiency of cisco feeding, so they packed on more body mass relative to the mercury they consumed.15Europe PMC. Spiny water flea invasion alters fish mercury bioaccumulation rates This is a rare case where an invasive species produced a partially positive outcome for fish, at least from a contaminant perspective, though the broader ecological disruption spiny water fleas cause remains a concern.
Contaminants are a long-running issue in Lake Ontario more broadly. The lake has historically carried some of the highest pollutant loads among the Great Lakes, and persistent chemicals like polychlorinated biphenyls (PCBs) accumulate through the food chain. Modeling of PCB congeners in lake trout showed that specific congener pairs can account for about 16% of the total PCB burden in Lake Ontario fish, with concentrations climbing as fish grow older and larger.16Elsevier. Application of a polychlorinated biphenyls bioaccumulation model to Lake Ontario lake trout For anglers, this translates to fish consumption advisories that vary by species, size, and location. Large, long-lived predators like lake trout carry higher contaminant loads than smaller, shorter-lived fish.
A Virus That Kills Dozens of Species
In April 2005, tens of thousands of freshwater drum turned up dead in the Bay of Quinte on Lake Ontario, along with large numbers of round gobies and a few muskellunge. The cause was a strain of Viral Hemorrhagic Septicemia Virus (VHSV-IVb), marking the first major mortality event linked to this virus in the Great Lakes.17Multidisciplinary Digital Publishing Institute (MDPI). Spread of the Emerging Viral Hemorrhagic Septicemia Virus Strain, Genotype IVb, in Michigan, USA VHSV-IVb went on to cause additional outbreaks in 2006, 2007, and 2008, affecting more than 30 freshwater fish species across the Great Lakes basin.18PubMed Central. Evolutionary trajectory of fish Piscine novirhabdovirus (=Viral Hemorrhagic Septicemia Virus) across its Laurentian Great Lakes history: Spatial and temporal diversification
The virus has continued to evolve since its appearance. Genomic analysis of VHSV-IVb isolates collected from 2003 through the present day shows a trend toward lower virulence over time, which may actually help the virus persist longer in host populations without triggering the mass die-offs that draw attention.19Public Library of Science. Genomic and immunogenic changes of Piscine novirhabdovirus (Viral Hemorrhagic Septicemia Virus) over its evolutionary history in the Laurentian Great Lakes For fish in Lake Ontario, VHS represents an ongoing background threat, one more pressure layered on top of everything else.
Climate Change and the Shifting Calendar
Lake Ontario is warming. Average summer water temperatures increased by over 1°C between the mid-1990s and 2019, from about 15.4°C to 16.4°C. This may sound minor, but it has measurable effects on fish behavior. A 27-year monitoring study at a fishway found that, across both native and non-native species, fish are arriving more than a week earlier in the season than they did in the late 1990s.20PubMed Central. Climate Change Impacts on the Phenology of Laurentian Great Lakes Fishes That shift in timing can create mismatches between predators and prey, between spawning fish and the temperature windows their eggs need, and between migrating species and the food sources they depend on at specific life stages.
The broader expectation is that coldwater species will decline while warmwater species expand their range and abundance. This means the native warmwater fish gaining ground in places like the Toronto waterfront may have tailwinds, while coldwater species, both native lake trout and stocked salmonids, face an increasingly hostile thermal environment. For a lake already struggling to support its original coldwater community, warming adds another dimension of difficulty.
Dam Removal and the Invasive Species Tradeoff
Many of Lake Ontario’s tributaries are fragmented by dams, and removing those barriers is a standard tool for restoring fish passage. Native migratory species like Atlantic salmon and lake sturgeon need access to upstream spawning and rearing habitat. But when you open a river, you open it to everyone. Research on dam removals in Great Lakes watersheds has documented round gobies spreading upstream into newly accessible habitat over a 14-year period following a single dam removal.21PubMed Central. A secondary upstream invasion of round goby in the Great Lakes Basin over fourteen years following a dam removal
Optimization-based analyses of dam mitigation strategies in river systems have found that accounting for invasive species when prioritizing which barriers to remove or modify is three to six times more expensive than simply maximizing native fish habitat.22Elsevier / PubMed Central. Prioritizing native migratory fish passage restoration while limiting the spread of invasive species: A case study in the Upper Mississippi River Managers around Lake Ontario face this calculation regularly: every barrier removed for salmon or sturgeon passage is a barrier removed for gobies, sea lampreys, and potentially other invasive species. Some tributaries now use selective fish passage structures that allow target species through while blocking others, but these are imperfect and expensive. The connectivity question sits at the heart of modern Great Lakes fisheries management, and there are no solutions that avoid tradeoffs entirely.