Today, a budding brook trout ecologist can feel overwhelmed by the amount of research that has already been done on their beloved species. And, truth be told, this feeling never goes away. Salmon species are one of the most popular research targets in fisheries. However, these previous studies, most of which conducted within the last 30 years, provide nearly the entire knowledge base on brook trout ecology and can still answer some of today's most burning questions.
Check back soon for literature to help address the following topics:
Check back soon for literature to help address the following topics:
- Why are brown trout bad?
- How fast are brook trout declining?
- Are hatcheries bad?
- The fish are there, but why can't I catch them?
- What makes good brook trout habitat?
Why are brown trout bad?

Borrowing a line from the infamous Gettysburg Address, natural resource management is a product “of the people, by the people, (and) for the people.” And, much like modern day politics, many management decisions quickly become contentious topics fueled by opposing viewpoints on how the environment should be managed.
In fisheries, one of the most debated topics is whether environments should be managed to support native diversity or recreational fisheries. Unfortunately, this is often an “or” rather than “and” decision as initiatives that improve native species conservation are often done at the cost of improving recreational fisheries. This sets the stage for the discussion on native brook vs. nonnative brown trout.
Let’s start with the positive. Brown trout are an excellent fishery. They are easy to grow in hatchery environments and, since introduction in the late 1800s, brown trout have established naturally reproducing populations. For many anglers, the species is a prized target. Economically, this means that brown trout are a great source of revenue as people are willing to spend a lot of money on tackle, fishing licenses, transportation, and lodging all for the chance to catch brown trout. And, the species is plentiful and grows quickly giving even the novice angler a chance for a memorable catch.
Ecologically, brown trout aren’t the Good Samaritans they may appear to be. Brown and brook trout require many of the same resources and, just like siblings, compete for access to food, shelter, and habitat. In ecology, two species with overlapping requirements (also known as their “ecological niche”) cannot coexist and the dominant competitor will drive out the subordinate.
In the case of brook and brown trout, brown trout almost always win. Brown trout grow faster and live longer than brook trout allowing their populations to quickly take the majority lead. Brown trout also prefer slightly warmer stream temperatures, pushing the competitive advantage further in their favor in summer months and in streams that are larger and shade from streambank tree cover. And, if we look ahead, climate change is expected to result in an increase in stream temperature, which will only continue to favor brown trout.
Where do brook trout go when they lose the fight? While some populations do completely die, usually brook trout move further upstream where temperatures are colder and brook trout can have a slight competitive edge over the warmer-water tolerant brown trout. However, these populations become isolated from one another and after many generations of inbreeding and loss of genetic diversity, their ability to survive environmental disturbance decreases and the population becomes at risk of dying.
Some argue that the competitive ability of brown trout places them as a more “worthy” species and that replacement of one trout species for another doesn’t alter overall ecosystem function and value. However, studies have shown that resource use at fine scales can differ dramatically between very closely related species. For example, one species of fish may prefer insects that are light enough to drift on top of the water while another prefers insects that sink into the water column. This difference still seems negligible; however, many stream insects originate on land where they are also food for terrestrial animals. So, if the nonnative fish eats the floating insects that would normally feed terrestrial organisms, than the presence of the nonnative can actually decrease the number of birds, spiders, bats, and other land animals. Suddenly it brook for brown may not seem like such an even trade.
Because brown trout have well-established populations it would be nearly impossible to remove them from most streams (at the very least it would be extremely expensive). Further, they are a great revenue source, often times paying for brook trout conservation initiatives. So, the struggle moving forward is determine how to conserve brook trout populations while managing brown trout invasion. It can be done, but requires understanding that the two are not compatible co-inhabitants. This doesn’t necessarily mean that brown trout need to be removed from an entire watershed. Minimizing stocking and/or targeted removals of brown trout in select streams while simultaneously maintaining brown trout in other streams has been shown to be a viable option for maintaining both species in close proximity.
In fisheries, one of the most debated topics is whether environments should be managed to support native diversity or recreational fisheries. Unfortunately, this is often an “or” rather than “and” decision as initiatives that improve native species conservation are often done at the cost of improving recreational fisheries. This sets the stage for the discussion on native brook vs. nonnative brown trout.
Let’s start with the positive. Brown trout are an excellent fishery. They are easy to grow in hatchery environments and, since introduction in the late 1800s, brown trout have established naturally reproducing populations. For many anglers, the species is a prized target. Economically, this means that brown trout are a great source of revenue as people are willing to spend a lot of money on tackle, fishing licenses, transportation, and lodging all for the chance to catch brown trout. And, the species is plentiful and grows quickly giving even the novice angler a chance for a memorable catch.
Ecologically, brown trout aren’t the Good Samaritans they may appear to be. Brown and brook trout require many of the same resources and, just like siblings, compete for access to food, shelter, and habitat. In ecology, two species with overlapping requirements (also known as their “ecological niche”) cannot coexist and the dominant competitor will drive out the subordinate.
In the case of brook and brown trout, brown trout almost always win. Brown trout grow faster and live longer than brook trout allowing their populations to quickly take the majority lead. Brown trout also prefer slightly warmer stream temperatures, pushing the competitive advantage further in their favor in summer months and in streams that are larger and shade from streambank tree cover. And, if we look ahead, climate change is expected to result in an increase in stream temperature, which will only continue to favor brown trout.
Where do brook trout go when they lose the fight? While some populations do completely die, usually brook trout move further upstream where temperatures are colder and brook trout can have a slight competitive edge over the warmer-water tolerant brown trout. However, these populations become isolated from one another and after many generations of inbreeding and loss of genetic diversity, their ability to survive environmental disturbance decreases and the population becomes at risk of dying.
Some argue that the competitive ability of brown trout places them as a more “worthy” species and that replacement of one trout species for another doesn’t alter overall ecosystem function and value. However, studies have shown that resource use at fine scales can differ dramatically between very closely related species. For example, one species of fish may prefer insects that are light enough to drift on top of the water while another prefers insects that sink into the water column. This difference still seems negligible; however, many stream insects originate on land where they are also food for terrestrial animals. So, if the nonnative fish eats the floating insects that would normally feed terrestrial organisms, than the presence of the nonnative can actually decrease the number of birds, spiders, bats, and other land animals. Suddenly it brook for brown may not seem like such an even trade.
Because brown trout have well-established populations it would be nearly impossible to remove them from most streams (at the very least it would be extremely expensive). Further, they are a great revenue source, often times paying for brook trout conservation initiatives. So, the struggle moving forward is determine how to conserve brook trout populations while managing brown trout invasion. It can be done, but requires understanding that the two are not compatible co-inhabitants. This doesn’t necessarily mean that brown trout need to be removed from an entire watershed. Minimizing stocking and/or targeted removals of brown trout in select streams while simultaneously maintaining brown trout in other streams has been shown to be a viable option for maintaining both species in close proximity.
How fast are brook trout declining?

Let’s talk a little about population dynamics first. In a loose sense, a population is a group of individuals of the same species that regularly interact with one another. For most species there are many different populations and where the boundaries of each population are “drawn” depends largely on how far the animal moves. So, for deer, we may talk about only a few populations per state, whereas for brook trout each stream is typically its own population (and sometimes many populations within a stream if there are barriers to movement, like waterfalls).
It’s quite natural for populations to “blink on and off,” meaning one year it may be completely gone but in a few more years the population recovers due to immigration of individuals from nearby populations. However, when the population never comes back, it is said to be extirpated. When enough populations become extirpated, the species becomes at risk for extinction. Scientists spend a lot of time monitoring populations to determine risk factors for extirpation, mostly notably the number of individuals in the population (we’ll come back to this subject another day, but suffice to say it’s harder to kill 1000 individuals than 10).
Right now brook trout, as a species, are not at risk of extinction. However, populations are becoming extirpated at an increasingly high rate. A study by Mark Hudy and colleagues in 2008 showed that 28% of historic brook trout populations are now extirpated and another 35% of populations have been reduced. That’s well over half of historic brook trout populations either gone or at risk of future extirpation. HALF!
The aforementioned study linked brook trout population size to watershed land use and specifically found that watersheds with more forested land are more capable of supporting brook trout populations. This method highlights Pennsylvania as one of the states hardest hit with nearly 90% of historic brook trout populations observed or predicted to be extirpated or significantly reduced.
Hudy and others paint a fairly dark picture for the future of brook trout. But, in the grand scheme of things, they weren’t even using the color black as their analysis didn’t touch on stream temperature rise. Brook trout prefer stream temperatures no higher than about 65°F. In the future, air temperature on the east coast is projected to increase by as much as 9°F. While stream and air temperature are not always closely related, a rise in air temperature will cause an increase in stream temperature and widespread loss of brook trout populations. This is particularly true in the southern range of brook trout in states such as Georgia and South Carolina where populations are already near thermal optima.
So, while brook trout are unlikely to go extinct while any of us are still roaming the streams, they are declining. And while these declines are biologically devastating, they are also felt economically and recreationally as anglers are now having to work harder to access trout streams. A study by DeWeber and Wagner showed that trout anglers in State College, PA will soon have to travel upwards of 200 miles to access a brook trout stream.
Will the fishery survive this hardship, or is the sport a pastime of older generations?
It’s quite natural for populations to “blink on and off,” meaning one year it may be completely gone but in a few more years the population recovers due to immigration of individuals from nearby populations. However, when the population never comes back, it is said to be extirpated. When enough populations become extirpated, the species becomes at risk for extinction. Scientists spend a lot of time monitoring populations to determine risk factors for extirpation, mostly notably the number of individuals in the population (we’ll come back to this subject another day, but suffice to say it’s harder to kill 1000 individuals than 10).
Right now brook trout, as a species, are not at risk of extinction. However, populations are becoming extirpated at an increasingly high rate. A study by Mark Hudy and colleagues in 2008 showed that 28% of historic brook trout populations are now extirpated and another 35% of populations have been reduced. That’s well over half of historic brook trout populations either gone or at risk of future extirpation. HALF!
The aforementioned study linked brook trout population size to watershed land use and specifically found that watersheds with more forested land are more capable of supporting brook trout populations. This method highlights Pennsylvania as one of the states hardest hit with nearly 90% of historic brook trout populations observed or predicted to be extirpated or significantly reduced.
Hudy and others paint a fairly dark picture for the future of brook trout. But, in the grand scheme of things, they weren’t even using the color black as their analysis didn’t touch on stream temperature rise. Brook trout prefer stream temperatures no higher than about 65°F. In the future, air temperature on the east coast is projected to increase by as much as 9°F. While stream and air temperature are not always closely related, a rise in air temperature will cause an increase in stream temperature and widespread loss of brook trout populations. This is particularly true in the southern range of brook trout in states such as Georgia and South Carolina where populations are already near thermal optima.
So, while brook trout are unlikely to go extinct while any of us are still roaming the streams, they are declining. And while these declines are biologically devastating, they are also felt economically and recreationally as anglers are now having to work harder to access trout streams. A study by DeWeber and Wagner showed that trout anglers in State College, PA will soon have to travel upwards of 200 miles to access a brook trout stream.
Will the fishery survive this hardship, or is the sport a pastime of older generations?
Are Hatcheries Bad for Brook Trout?

It started in the 1800s. As pioneers moved west, so did human influence of natural ecosystems. Among them, increased fishing pressure on otherwise untouched rivers, ponds, and streams. However, not long after the first line was cast, fish stocks took a sharp decline and started mirroring their eastern counterparts that were left limping after centuries of limitless harvest. In some of the first studies of fisheries, biologists were tasked with determining the cause of fish declines. The smoking gun was clear: overharvest. And, the proposed solution would forever change the way we manage fish.
The first fish hatchery, Baird Hatchery, was built on the McCloud River in California in 1872. It was in part the brainchild of President Ulysses S. Grant, who was in office during the first government movements to conserve U.S. fishery resources. Grant elected Spencer Baird the first United State Commissioner of Fisheries, and one of Baird’s goals was to replenish declining fish stocks on the east coast.
The answer, Baird believed, was Pacific salmon, and he sent Livingston Stone to California in search of salmon spawning grounds. Locals directed Stone to a spot on the McCloud River where they had seen spawning salmon and, once confirmed, Stone started construction on Baird Hatchery. In the years that followed, millions of salmon and rainbow trout eggs were collected, incubated, and shipped all around the country on railroads where they were then stocked, often into nonnative waters. At the time hatcheries seemed like a savior to natural resources- a free ticket to continue overfishing. However, today, hatcheries have become a contentious topic with many wishing for an end to the industry.
The first fish hatchery, Baird Hatchery, was built on the McCloud River in California in 1872. It was in part the brainchild of President Ulysses S. Grant, who was in office during the first government movements to conserve U.S. fishery resources. Grant elected Spencer Baird the first United State Commissioner of Fisheries, and one of Baird’s goals was to replenish declining fish stocks on the east coast.
The answer, Baird believed, was Pacific salmon, and he sent Livingston Stone to California in search of salmon spawning grounds. Locals directed Stone to a spot on the McCloud River where they had seen spawning salmon and, once confirmed, Stone started construction on Baird Hatchery. In the years that followed, millions of salmon and rainbow trout eggs were collected, incubated, and shipped all around the country on railroads where they were then stocked, often into nonnative waters. At the time hatcheries seemed like a savior to natural resources- a free ticket to continue overfishing. However, today, hatcheries have become a contentious topic with many wishing for an end to the industry.
So, what’s the problem with hatcheries? While hatcheries can be used to successfully supplement natural populations, that end goal is rarely realized. Up to 99% of stocked fish die within a month of being released. The cause of mortality can vary, but in many instances fish die because they don’t know how to ‘be a fish.’ The life of a fish in a hatchery involves swimming in a concrete raceway with thousands of other fish and waiting for someone to throw handfuls of pellet food into the tank. However, once released, life is much different. Fish suddenly find themselves in the presence of predators (which they cannot identify, nor avoid), in a variable environment with frequent changes in flow, temperature, and food patchiness, and surrounded by insects they don’t identify as food. Some researchers have even observed hatchery fish die in a wild stream after filling their stomachs with rocks that look like food pellets. The weight of all the rocks anchored the fish to the stream bottom, making it impossible for them to swim.
Because hatcheries are paid by the fish, a problem often encountered is a “quantity over quality” approach to hatchery management. Hundreds of millions of dollars are spent annually on hatcheries to increase stocking densities and, while the cost per fish may be low, the high mortality rate means that the cost per SURVIVING fish could be upwards of $300. Put another way, for $300 hatcheries might get one single fish that reproduces and hundreds of dead fish floating downstream.
Because hatcheries are paid by the fish, a problem often encountered is a “quantity over quality” approach to hatchery management. Hundreds of millions of dollars are spent annually on hatcheries to increase stocking densities and, while the cost per fish may be low, the high mortality rate means that the cost per SURVIVING fish could be upwards of $300. Put another way, for $300 hatcheries might get one single fish that reproduces and hundreds of dead fish floating downstream.
While improving survival and reproduction of hatchery fish may seem like a logical goal, ironically, reproduction of stocked fish is often one of the last things managers want to see in the wild. Natural populations are adapted to local conditions, and their genetics reflect many generations of evolution and natural selection of traits to best match that environment. When fish spawn, these traits are ‘handed down’ to their offspring, giving them the traits they need to survive and thrive in that environment.
By comparison, hatchery fish are often inbred and have low genetic variability. They are adapted for hatchery environments, which often means selection for fish that grow fast and have resistance to diseases commonly seen in hatcheries (but frequently rare in the wild). When a hatchery fish breeds with a native fish, the offspring are handed down a mixed bag of traits that makes them less successful at living in the wild in comparison to their purebred counterparts. This phenomena, known as outbreeding depression, can decrease genetic diversity of natural populations, which decreases population health and increases risk of collapse. And, the effects of stocking are long-lasting as it can take many generations of natural reproduction to reverse the effects of outbreeding depression.
So, do hatcheries have a place in fisheries management? Absolutely. However, it’s not as simple as putting fish where people want them. Where native fish populations are present, stocking can accelerate population decline and result in native fish extirpation. However, the goals of hatchery stocking are further reaching that just angling. Restorative stocking, which aims to increase long-term health and establish reproducing populations have been particularly beneficial for conservation of collapsing populations. For example, hatcheries have been used to supplement natural populations of the endangered razorback sucker. In these instances, hatcheries have conducted careful genetic studies to ensure stocked populations are well-suited for the environment they are released in to and breeding between wild and hatchery stocks will not result in outbreeding depression.
By comparison, hatchery fish are often inbred and have low genetic variability. They are adapted for hatchery environments, which often means selection for fish that grow fast and have resistance to diseases commonly seen in hatcheries (but frequently rare in the wild). When a hatchery fish breeds with a native fish, the offspring are handed down a mixed bag of traits that makes them less successful at living in the wild in comparison to their purebred counterparts. This phenomena, known as outbreeding depression, can decrease genetic diversity of natural populations, which decreases population health and increases risk of collapse. And, the effects of stocking are long-lasting as it can take many generations of natural reproduction to reverse the effects of outbreeding depression.
So, do hatcheries have a place in fisheries management? Absolutely. However, it’s not as simple as putting fish where people want them. Where native fish populations are present, stocking can accelerate population decline and result in native fish extirpation. However, the goals of hatchery stocking are further reaching that just angling. Restorative stocking, which aims to increase long-term health and establish reproducing populations have been particularly beneficial for conservation of collapsing populations. For example, hatcheries have been used to supplement natural populations of the endangered razorback sucker. In these instances, hatcheries have conducted careful genetic studies to ensure stocked populations are well-suited for the environment they are released in to and breeding between wild and hatchery stocks will not result in outbreeding depression.

Stocking of sterile adults has also risen in popularity as a way to increase population sizes or create angling opportunities without the risk of the negative effects discussed above. Originally native to Asia, grass carp consume underwater vegetation, and sterilized forms are now commonly introduced into reservoirs and ponds to remove nonnative vegetation and improve overall ecosystem health. Even sterilized hybrids, such as tiger trout (brook x brown) can be raised in hatcheries and introduced to improve recreational fisheries.
Finally, research has shown that training hatchery fish to ‘be fish’ can dramatically increase survival after release. Something as simple as making rearing tanks more unpredictable by adding structure or mimicking predation can increase performance in the wild. However, hatcheries that incorporate these changes often require rearing fewer individuals at a time, and may increase operating costs per fish. However, taking a “quality over quantity” approach to hatcheries, along with a consideration for genetic stocks, could increase the efficacy of using hatcheries for both angling and conservation.
Finally, research has shown that training hatchery fish to ‘be fish’ can dramatically increase survival after release. Something as simple as making rearing tanks more unpredictable by adding structure or mimicking predation can increase performance in the wild. However, hatcheries that incorporate these changes often require rearing fewer individuals at a time, and may increase operating costs per fish. However, taking a “quality over quantity” approach to hatcheries, along with a consideration for genetic stocks, could increase the efficacy of using hatcheries for both angling and conservation.