The Rainbows of Bristol Bay

Research on the rainbow trout of Bristol Bay reveals the complexity of this watershed.

The signs of the feast are everywhere. It’s the sockeye salmon spawn in Bristol Bay, and creatures large and small are taking advantage of the bounty. The grizzly bears are most conspicuous, strolling along the river. In places, you’ll see lines of salmon carcasses lining the bank, each with a large chomp mark out of its side.

Bald eagles and gulls sit on dead salmon wherever you look, and even a furtive red fox might sneak in to grab a snack.

You might not notice, but there’s a feast underwater, too. The red sockeye salmon are quite visible, finning in the depths. Just downstream, predatory fish gulp the salmon eggs and chunks of decomposing salmon flesh that float downstream. For those of us inclined to carry fishing rods, this presents one of the greatest outdoor experiences on the planet.

I’ve had the great fortune to drift egg patterns on salmon rivers, connecting to the feeding frenzy under the surface. Among the most frequent catches are rainbow trout. Big, bulky rainbow trout, gorging on lipids.

The rainbow trout is one of the most familiar gamefish worldwide, stocked far and wide and in great numbers. If you’re an angler, it can feel like you know all you need to know about rainbows. But here in Bristol Bay, rainbows still hold surprises. In fact, researchers studying rainbow trout have found that these fish can help reveal just how complex and intertwined this system is.

aerial view of forest, river and distant mountains
Aerial views of the Bristol Bay watershed in southwest Alaska, near the location of the proposed Pebble Mine. © Bridget Besaw / TNC

The Salmon Ecosystem

Bristol Bay is home to half the world’s sockeye salmon. The annual spawning runs of these fish influence an entire region: the wildlife and the people and even the land. As The Nature Conservancy in Alaska puts it:

“Everything runs on wild salmon in Alaska’s Bristol Bay. Nature runs on salmon. Communities. Business and industry. Salmon is the basis of millennia-old Indigenous traditions. The lands and waters of Bristol Bay produce more wild salmon than anywhere else on Earth and that fuels a sustainable commercial salmon fishery valued at $1.5 billion annually.” 

Bristol Bay has also been in the news for another reason: the proposed Pebble Mine, a gigantic mining operation that would be located in the headwaters in the ecosystem. There have been many twists and turns in the mine proposal, as Alaskan Natives, sport anglers and hunters, commercial fishers, environmental groups and others opposed the mine for its potentially devastating impacts.

aerial view of Alaskan watershed
Under an overcast sky, an aerial view of the rugged Bristol Bay watershed in the area of the proposed Pebble Mine development in southwest Alaska. © Bridget Besaw / TNC

In August, the U.S. Army Corps of Engineers found that the Pebble Mine cannot be permitted under the Clean Water Act. It was a positive step for conservation, but the fight isn’t over.

To understand what’s at stake, researchers need to understand the complexity of a system like Bristol Bay. At a glance, conserving Bristol Bay’s watersheds might seem to be all about salmon. In reality, there are many interconnected pieces to the puzzle. Take rainbow trout.

To discuss rainbow trout, I turned to researcher Martin Arostegui. Arostegui may be one of the ultimate fish nerds. A well-known angler, he’s caught literally hundreds of fish species around the globe. He holds the fourth-highest number of fishing records recognized by the International Game Fish Association. (The only people with more records are his parents and a close friend). Last year, he completed his Ph.D. at the University of Washington’s School of Aquatic and Fishery Sciences, with a focus on studying the life histories of rainbow trout in streams and lakes of the Bristol Bay drainage. In the past two years, he’s published four articles in the literature detailing his findings.

Martin Arostegui during fieldwork in Alaska. © Rachel Hovel

Rainbow trout can exhibit very different life histories. Most anglers are well acquainted with the stream-resident and anadromous forms, commonly known as steelhead. These fish are both extensively studied and subject to intense management attention. Much less is known about lake-migrant rainbow trout, with the exception of some well-studied fisheries like Kootenay Lake in British Columbia.

In the Bristol Bay watershed, lake-migrant rainbow trout swim alongside stream-resident forms. They look and behave differently. Even though Bristol Bay’s rivers and streams connect to the ocean, you won’t find steelhead.

“There’s no barrier to migration,” Arostegui explains. “But the rainbow trout don’t seem to go to the ocean. And that’s because they don’t need to go. They get ample food resources by staying in freshwater.”

That food, of course, is in the form of sockeye salmon.

Decomposing salmon feed an ecosystem. © Matthew L. Miller

Stream or Lake?

The sockeye salmon run represents an annual influx of calories upon which both stream-form and lake-migrant trout binge. But why do some rainbow trout spend all their time in streams, while others migrate to lakes?

“Just as with steelhead and stream-resident trout, there are advantages and trade-offs,” says Arostegui. “If you stay resident in the stream, there may not be as much food, but you stay safer. You’re smaller so you may not be as attractive to predators. Prior to the sockeye salmon migration, these fish are eating very different prey.”

Stream-resident fish feed primarily on aquatic and terrestrial insects when sockeyes aren’t around. Lake-migrant forms have access to the abundance of amphipods, snails and other diverse prey. Stream fish contend with a variety of other fish species for the same food resources, while lake migrants only compete and partially overlap in diet with Arctic char. This enables lake-migrant trout to bulk up more than their stream counterparts.

fish in a net
Alaskan rainbow trout. © Matthew L. Miller

“If you’re a trout in a lake, you have to contend with predators like freshwater harbor seals and large Arctic char,” he says. “But when it comes time to spawn, you’re very large. Such a male is very competitive and can have access to lots of females and their eggs. Similarly, larger females produce more and larger eggs, increasing their chances of successfully producing offspring.”

The lake-migrant rainbows behave much like steelhead. That’s because, as Arostegui’s research published in the journal Molecular Ecology shows, these lake-form fish often retain the genetic signature associated with steelhead.

“These fish don’t go to the ocean anymore” says Arostegui. “But their genetics suggest they still have the ancestral ability to osmoregulate. The fish in lake and stream look very different from each other in both coloration and morphology.”

The author’s father with Alaskan rainbow trout. © Matthew L. Miller

Conservation Implications

Does it matter that there are different forms of rainbow trout? Or is it just a neat detail for a fish nerd like me?

It actually matters a great deal, and indicates just how complex a functioning ecosystem is. And also how difficult it would be to put such an ecosystem back together if it is damaged or degraded.

The diversity within rainbow trout makes the species quite resilient to the fluctuations of a dynamic ecosystem. If a sockeye salmon run is down in one part of the system, it might affect some trout. But lake-migrant trout move around the system and can take advantage of salmon wherever they are.

Perhaps more important, rainbow trout diversity shows the interplay between habitat and genetics.

“If you remove habitat diversity, you reduce life history diversity and thus the overall stability of the ecosystem,” says Arostegui.

red salmon in reeds
A sockeye salmon. © Matthew L. Miller

But the genetic diversity is important too. “There is a lot of diversity within a population that can be unappreciated,” says Arostegui. “If you lose the genetic diversity, you don’t get it back. You might restore habitat, but you are still missing critical components of the ecosystem. You need to think about habitat and genetic diversity.”

Ecologist Aldo Leopold famously noted “to keep every cog and wheel is the first precaution of intelligent tinkering.” As conservation biologists study ecosystems, it becomes apparent that keeping every cog and wheel is far more difficult than it first appears.

If an ecosystem suffers damage – say from a mine leak – and loses a lot of rainbow trout, it might seem like you can restore the ecosystem simply by reintroducing rainbow trout. But the complex genetics within the population isn’t replaced. It’s like trying to reassemble Humpty Dumpty but with large pieces of shell missing.

Similar life history and genetic diversity have been found with sockeye salmon, Arctic char, Dolly Varden and other species in the Bristol Bay watershed. It isn’t just the diversity of species; it’s the diversity within species. For many ecosystems, that genetic diversity is already lost. The best we can do is reassemble a facsimile of what was once there. But that’s not the case in Bristol Bay.

“This system is essentially pristine,” says Arostegui. “There haven’t been hatcheries or transplants. There haven’t been significant alterations to the habitat. When most people talk about salmonid habitat, they talk about rivers. But lakes are also absolutely critical to salmonids. People think about salmon, but rainbow trout are so important too. This diversity makes the ecosystem more resilient, and the parts are still there in Bristol Bay.”

Published on


Arostegui, Martin & Quinn, Thomas. (2018). Trophic ecology of nonanadromous rainbow trout in a post-glacial lake system: Partial convergence of adfluvial and fluvial forms. Canadian Journal of Zoology. 96. 10.1139/cjz-2017-0201.

M C Arostegui, T P Quinn, Ontogenetic and ecotypic variation in the coloration and morphology of rainbow trout (Oncorhynchus mykiss) in a stream–lake system, Biological Journal of the Linnean Society, Volume 128, Issue 3, November 2019, Pages 681–699,

Arostegui, MC, Quinn, TP, Seeb, LW, Seeb, JE, McKinney, GJ. Retention of a chromosomal inversion from an anadromous ancestor provides the genetic basis for alternative freshwater ecotypes in rainbow trout. Mol Ecol. 2019; 28: 1412– 1427.

Arostegui, MC, Quinn, TP. Reliance on lakes by salmon, trout and charr (Oncorhynchus, Salmo and Salvelinus): An evaluation of spawning habitats, rearing strategies and trophic polymorphisms. Fish Fish. 2019; 20: 775– 794.

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  1. Michael McLaughlin says:

    This author wrote of the Salmon as if they only existed as food or exploitation. This psychopathic failure to recognize either species of fish subjects of the essay illustrates the inherent problem of the preset culture.
    For 18 Million years the semelparous salmon have come to their natal streams to reproduce. The damming, the fossil fuel extraction the greedy and toxic mining (processing ores use extremely toxic chemicals/elements).
    Semelparous means reproducing only ONCE in a lifetime, although rare salmon have been noted as surviving their reproductive stint, returning to the sea and becoming iteroparous- perhaps once more, but we are not sure.

    Salmon once ran from the Arctic’s McKenzie to California’s San Buenaventura (Ventura) watersheds, with probable presence as far as the Santa Ana, that drains the southern San Gabriels and San Jacinto massifs during the Pleistocene.

    Of course, they also run as far south as the Korean area of Asia, and the Norway and Scotland area of Europe.
    Extreme pressure from commercial fishing by Chinese interests have caused salmon to be offered to the immense overpopulation of humanity, while their populations in the dammed rivers are or have been winking out like lights forever lost.
    “Farming” consists of huge industrial efforts as well as grinding up domestic livestock and other fish[stock] to artificially feed these species, which normally feed far lower on the food web. That farming introduces accidental unadapted fish, promotes parasite populations (the farming- or more accurately, massive industrial equipment looking quite like the buildings of pipes left forever on Alaska’s North slope defunct oil stations) that kill a majority of wild young parr and smolt- early freshwater stages of salmon before they develop full osmoregulation.

    With every significant published article referencing “outdoors” – a peculiar term, as the real world essentially exists without doors (as opposed to the contrafactual ideations in the minds of the species I target through this communication), we find increasing and quite artificial selective exploitative pressure on formerly balanced ecosystems.

    Any single watershed can only accommodate a small number of human takers without additively increasing anadromous fish mortality and further hunger-stressing the organisms tht depend upon salmon and other spawning aquatic animals.

    Long before the atrocious fish “farms” mentioned, I made it a point to NEVER eat salmon or other organisms unless I was living where they ran, and hope that others will cease to reach out inordinately from their own home ranges and territories to colonize the living world, extracting without giving back.

    Many humans differentiate themselves from those they term “indigenous” but only the observational awareness exhibited by those who maintain the tradition of taking only a small part- even the greatest land predators take only about 1 in six to twelve of their prey across a prey species lifetime, and should there be observable diminution, we should CEASE.

    These lives are NOT “sport” for the killing, but have intrinsic worth, and just as ANY of you both feel pain, and do NOT wish to die before the tie of their life’s fulfillment.

    ‘s Norht Slope following cessation fo oil pumping)

  2. Fletcher Hahn says:

    Fascinating discussion of the delicate balance of land, water, fish and mammals in the Bristol Bay watershed. I have always opposed the Pebble Mine, and now my opposition is reinforced. Great piece!

  3. John Tuxill says:

    As one who has been similarly fortunate to fish for Bristol Bay rainbow trout, I enjoyed this article greatly. One very distinctive regional feature that you don’t mention (by name anyway) is Iliamna Lake–the largest freshwater lake in Alaska–directly downstream of the Pebble Mine site. Are the lake-form rainbow populations profiled here limited to the Iliamna watershed, and thus a product of the lake’s unique ecology and natural history? Or do they also occur in other Bristol Bay watersheds? Are there freshwater harbor seal populations in other lakes too?

    1. There are other lakes, although this paper did focus on Iliamna. Iliamna has its own harbor seal poulation.

      Rainbow trout are indigenous to a variety of lakes throughout their range. Most are not well studied. Thanks for writing.