What Happened to the Smelt in Lake Michigan?

Rainbow smelt populations in Lake Michigan collapsed in the late 1990s and early 2000s and have stayed at historic lows ever since. Federal surveys from 2023 and 2024 show biomass densities of large smelt hovering near zero, with weak year-classes of young fish offering little sign of recovery. The crash was not a single event with a single cause. It involved stocked predators consuming smelt faster than they could reproduce, invasive mussels gutting the base of the food web, and the disappearance of key prey organisms that smelt themselves depended on. The story of Lake Michigan’s smelt is really a story about how profoundly the lake’s entire ecosystem has been reshaped over the past half century.

How Smelt Arrived and Thrived

Rainbow smelt are not native to the Great Lakes. They were first recorded there in the 1910s, and the standard account credits a government introduction in Michigan around 1912. Recent genetic work has complicated that narrative: DNA analysis suggests the 1912 stocking accounts for only about half the ancestry of Great Lakes smelt, with the rest tracing to an anadromous (sea-run) source population. Gene flow among smelt across the Great Lakes appears to be high, with no strong genetic differences from lake to lake.¹

However they got there, smelt exploded across the Great Lakes in the decades that followed. By the 1940s, they had become a fish of primary importance to commercial fishermen and sport dippers alike. In Green Bay alone, commercial nets hauled in more than four million pounds in peak years, and the amateur dip-net harvest during spawning runs was even larger, reaching as much as five and a half million pounds in a single year in Michigan.² Spring smelt runs became community events in towns along the lakeshore, drawing crowds with lanterns, buckets, and deep fryers. For decades, smelt were as much a cultural fixture as an ecological one.

What Smelt Ate and Who Ate Them

Smelt are opportunistic predators. In Lake Michigan, their diet shifted with the seasons and with what was available at different depths. In spring, they fed heavily on calanoid copepods, and in summer, larger smelt switched to the opossum shrimp Mysis, a deep-water crustacean that was once a critical energy source throughout the lake.³ Studies in Lake Erie found that smelt also ate chironomid larvae and pupae, small fish, and various zooplankton, giving them a broader diet than many of the native planktivores they lived alongside.⁴

That dietary flexibility made smelt successful, but it also placed them squarely in the middle of the food web. Smelt and alewives together dominated the planktivorous fish community in Lake Michigan and became the primary food of lake trout and the Pacific salmon species (chinook, coho, steelhead) that fisheries managers stocked beginning in the 1960s.⁵ Smelt were simultaneously a nuisance species that damaged native fish and a forage species that the lake’s prized sportfish depended on. That dual identity made their population trajectory a matter of intense interest to managers trying to balance competing goals.

The Predation Squeeze From Above

The massive salmon stocking program that began in the late 1960s was designed in part to control alewife populations, which had themselves become a runaway invader. But stocked salmon and lake trout do not pick just one prey species. They eat whatever forage fish are available, and smelt were very much on the menu. As predator numbers built through the 1970s and 1980s, they exerted increasing pressure on both alewives and smelt.

A parallel situation played out in Lake Superior, where successful lake trout stocking in the 1970s was followed by a sharp smelt decline around 1980. Adult smelt suffered heavy mortality, and recruitment of young fish dropped off, pushing the population to historic lows for several years and reducing the food base for the very predators that had driven the decline.⁶ Lake Michigan’s smelt did not crash as abruptly in the 1980s, but predation pressure was ratcheting up and would become one leg of a multi-pronged collapse in the decades to come.

The Mussel Invasion and the Food Web It Destroyed

If predation from above was one blade of the scissors, the collapse of the food web from below was the other. Zebra mussels arrived in the Great Lakes in the late 1980s, followed by quagga mussels, which proved far more damaging. Quagga mussels colonized enormous swaths of Lake Michigan’s lake bed, including deep offshore zones that zebra mussels never reached. Their filter feeding shifted the lake’s energy from the open water column down to the bottom, starving the plankton community that had supported the entire pelagic food web.⁷

Ecosystem modeling has shown that mussel filtration, combined with declining nutrient loads from pollution-control efforts dating to the 1972 Great Lakes Water Quality Agreement, reduced primary productivity in Lake Michigan’s offshore zone. The effects radiated up the food web, causing resource limitation for prey fish and their predators alike.⁸ For smelt, this meant less zooplankton to eat and fewer of the deep-water invertebrates they relied on in summer.

The Disappearance of Diporeia

One of the most consequential casualties of the mussel invasion was Diporeia, a tiny amphipod that once carpeted the deep lake floor. Diporeia was an energy-rich food source for a whole suite of bottom-feeding and mid-water fish, including bloater, sculpin, alewife, and smelt. When quagga mussels spread across the lakebed, Diporeia populations crashed, falling to near zero in large areas of southern Lake Michigan.

Research comparing fish condition across sites with different Diporeia densities found clear effects. In areas where Diporeia had essentially vanished, fish switched to lower-quality alternative prey, and species like deepwater sculpin and large alewives had lower energy density, meaning less fat and less nutritional value per fish.⁹ For smelt, the loss of Diporeia meant one fewer high-quality food item in an already shrinking pantry. This nutritional squeeze likely reduced growth rates, body condition, and reproductive output, making smelt populations less resilient to all the other pressures hitting them simultaneously.

Where the Numbers Stand Now

Federal monitoring surveys tell a stark story. Large rainbow smelt (90 mm or bigger) have been at persistently low biomass in Lake Michigan since 2001. In the 2023 surveys, large smelt biomass was below 0.05 kilograms per hectare, and the young-of-the-year class was weak.¹⁰ The 2024 surveys showed a slight bump for large smelt in one survey method (0.21 kg/ha in acoustic surveys) but continued low numbers in bottom trawls (0.03 kg/ha), with small smelt also remaining scarce.¹¹

To put those numbers in perspective, these are fractions of what surveys recorded in the 1980s and early 1990s. There is no recovery trend. Year after year, smelt show up in trace amounts, with occasional marginally better year-classes that never seem to rebuild the population. The conditions that drove the collapse are all still in place: quagga mussels remain dominant, Diporeia has not returned, and predator stocking continues, though at reduced levels compared with the heyday of the salmon program.

The Damage Smelt Did on Their Way Up

Before their crash, smelt were themselves a destructive invasive species. One of their most damaging behaviors was predation on the larvae of native coregonid fishes, particularly lake whitefish and lake herring. Research in Twelve Mile Lake, Ontario, documented the severity: during peak larval abundance, whitefish and herring larvae appeared in 93% of smelt stomachs that contained food, with an average daily consumption of 8.4 larvae per smelt. Modeling suggested that the combined effect of smelt predation and natural mortality could drive whitefish recruitment to zero.¹²

Laboratory experiments confirmed the mechanism. Post-spawned adult smelt readily consumed larval whitefish from hatch size (around 12 mm) up to roughly 34 mm, achieving 100% predation efficiency on newly hatched larvae. Predation efficiency declined only as whitefish larvae grew large enough to exceed the smelt’s gape width.¹³ The timing was brutal: smelt spawn in spring, and their post-spawning feeding frenzy coincides precisely with the period when whitefish larvae are small and vulnerable. For decades, this predation was considered a primary driver of recruitment failure in lake whitefish populations across lakes where smelt had established themselves.

The Thiaminase Problem

Smelt also harmed predator fish indirectly through their body chemistry. Rainbow smelt contain high levels of thiaminase, an enzyme that destroys thiamine (vitamin B1). When salmon and lake trout eat large quantities of smelt, they can develop thiamine deficiency, a condition linked to reproductive failure, poor egg survival, and abnormal fry development. This has been identified as a major barrier to lake trout restoration in the Great Lakes.¹⁴

Analysis of forage fish from Lake Michigan found that thiaminase activity was greatest in gizzard shad, spottail shiners, alewives, and rainbow smelt. The thiamine content of these fish was actually above the dietary requirements of coldwater predators, so the problem was not a lack of vitamin B1 in the food. The problem was that the thiaminase enzyme destroyed the thiamine before predators could absorb it. Because alewives and smelt were the dominant prey, they were identified as key drivers of thiamine deficiency in Lake Michigan’s salmon and trout.¹⁵

Recent research has even found that consuming smelt is associated with changes in heart morphology in wild lake trout, suggesting the physiological consequences of a high-thiaminase diet extend beyond reproductive health.¹⁶ This is a case where the decline of smelt may actually have had some upside for the predator species managers are trying to restore. With fewer smelt in the diet, lake trout are potentially exposed to less thiaminase, though alewives remain a major source of the enzyme.

Parasites as a Recurring Stressor

Disease has periodically hammered smelt populations across the Great Lakes, though it is harder to pin down how much parasites contributed to the Lake Michigan decline specifically. The best-documented cases come from Lake Erie. A microsporidian parasite called Glugea hertwigi was observed in 90% of distressed young-of-the-year smelt during a mortality event and was considered a major contributing factor.¹⁷ Earlier sampling of dead and obviously stressed smelt in Lake Erie found parasite cysts heavily loading the intestines and gonads. Over 97% of affected males and about 77% of affected females were heavily infected, and the parasite load appeared to worsen the normal post-spawning die-off into something catastrophic.¹⁸

Glugea and other parasites are endemic in smelt populations throughout the Great Lakes. Whether parasite outbreaks in Lake Michigan contributed to the decline is unclear from the available data. But parasites tend to hit hardest when fish are already nutritionally stressed and crowded into suboptimal habitat, so it is plausible that the food-web disruptions caused by mussels and the loss of Diporeia made smelt more susceptible to disease even if parasites were not the primary driver of the collapse.

Early Life History and Why Recovery Is Difficult

Smelt spawn in spring, typically in tributary streams or over shallow nearshore gravel. Newly hatched larvae are tiny and spend their first weeks in shallow water before dispersing offshore through June and into August. By late August, young-of-the-year concentrate inshore again.¹⁹ That early life stage is when smelt are most vulnerable to starvation if zooplankton densities are too low, and to predation by the round goby and other nearshore species that were not in the lake when smelt were at their peak.

The fact that smelt larvae need productive, plankton-rich nearshore water during their first weeks of life puts them at a disadvantage in today’s Lake Michigan. Quagga mussels have cleared the nearshore water to an almost eerie transparency, and spring plankton blooms are weaker than they once were. A smelt larva hatching today faces a leaner environment than its counterpart from the 1980s did, and the chain of survival from egg to juvenile to adult is long enough that even a modest reduction in early survival can keep the population pinned at low levels for years.

Contaminants in the Food Chain

Before smelt numbers collapsed, they played a role in moving mercury and other contaminants up the Lake Michigan food chain. Sampling of forage fish in the mid-1990s found that smelt had a mean total mercury concentration of about 35 nanograms per gram of wet tissue, lower than alewives or bloaters. With the exception of a few species, nearly all the mercury in these forage fish was in the form of methylmercury, the more toxic and bioaccumulative form. Researchers noted that the Lake Michigan food chain was particularly efficient at transferring methylmercury to higher trophic levels compared with some inland lakes.²⁰ With smelt now a minor component of the forage base, their direct contribution to mercury loading in top predators has diminished, but the broader bioaccumulation pathway through alewives and other species persists.

A Lake That Keeps Changing

The smelt decline is one chapter in a much larger transformation. Lake Michigan in the 2020s looks nothing like the lake of the 1970s. The water is dramatically clearer. The deep, cold zones are less productive. The nearshore alternates between nuisance algal blooms and barren stretches of mussel-encrusted rock. Native species like lake whitefish, which suffered under smelt predation for decades, now face their own set of problems as the food web has reorganized around invasive mussels rather than the plankton-based system of the past. Whether smelt ever rebound depends on factors largely outside anyone’s direct control: the trajectory of quagga mussel populations, the potential for new invasive species, and the long-term effects of warming water temperatures on thermal habitat. For now, the fish that once drew thousands of people to the lakeshore with dip nets and headlamps on spring nights is a ghost in the trawl surveys, present in name but essentially absent in substance.