Nonnative Fish: Still the #1 Threat to Native Fish

A nonnative smallmouth bass caught from critically endangered Atlantic salmon habitat in Downeast Maine, with two small wild native brook trout removed from its stomach. Photo: Downeast Salmon Federation
In 2019, I wrote about nonnative fish, arguing that they are the number one threat to wild native trout. The title, “Fish, Fish, Fish: The Number One Threat to Native Trout,” was meant to be a play on words, not an absolute position. It was a philosophical challenge to the statement “Habitat, Habitat, Habitat” being used by a trout conservation group at the time, as well as the lack of focus on nonnative fish, especially nonnative trout.
Competition Kills
Of course, without sufficient habitat there will be no wild native trout. Healthy riparian areas, canopy, instream structure, connectivity, spawning habitat, forage, and cold, clean, well oxygenated water all contribute to providing the habitat needed to support wild native trout.
However, while habitat is critical, a lack of competition from nonnative fish, including trout, is equally important, and in many cases more so. As we have seen, wild native trout populations have been severely degraded, or worse, by the presence of nonnative fish, even when the habitat is suitable. Conversely, wild native trout are able to persist, and even prosper, in places where the habitat is not ideal. This includes low-gradient streams, shallow ponds, estuaries, beaver ponds, heavily altered streams, and even irrigation ditches, all of which lack some of the ideal habitat components noted above.
I have found wild native trout in streams that experience intermittency, lack canopy, sans instream structure, and where passage is inhibited, or even blocked, due to poorly designed culverts, bridges and other manmade structures, dry-top beaver dams, downed trees, and natural barriers such as waterfalls.
Conversely, I have found rivers and streams with ideal trout habitat that had a depressed wild native trout population, or no wild native trout at all. In almost all of these cases, it was the presence of nonnative fish that caused the decline or loss of the wild native trout.

The Swift River, in New Hampshire’s White Mountains, offers marginal habitat for its native brook trout. Photo: Philip N Young, via CC BY-NC-ND 2.0
Natural Habitat Challenges
I spend a lot of time on small headwater freestone streams in New Hampshire’s White Mountains. While these streams look like ideal trout habitat to the untrained eye, they lack much of what makes habitat suitable to wild native trout. Water flows run from extreme flooding to drought, with ideal flows the exception rather than the rule. The granite-lined streambeds are notably wider than the stream itself due to seasonal scouring, which limits the canopy and allows the water to warm. Woody debris is rare and in many cases virtually non-existent.
Classic trout spawning habitat is rare, and fish often must travel great distances to find it. These first- and second-order streams are tributary poor, and most of the feeders you do find are short due to natural waterfalls and subject to intermittency in the late summer and fall, a period that is critical to spawning native brook trout.
While the downstream movement of fish is never completely blocked, upstream movement in these streams is often cut off by natural obstructions that have existed for eons. And in many cases, there are numerous barriers, often separated by just a couple of hundred feet.
As the water warms in the summer, the wild native brook trout that call these streams home push upstream in search of thermal refuge until they can’t go any farther. Come winter, these streams freeze from the top and bottom, referred to as anchor ice, leaving just a small ribbon of water flowing under the ice shelves.
Most of the streams I fish would be considered forage-poor. Aquatic insect life is limited, and notable hatches are virtually nonexistent. The substrate is not conducive to burrowing insects, and habitat for swimming and clinging insects is limited by the greatly fluctuating flows that scour the streambed. Leeches and crayfish are rare, and non-trout minnows are outnumbered by trout 100-to-1. Much of the available forage comes from above in the form of ants, beetles, caterpillars, and moths.
In most cases, nonnative fish, including trout, are not present in these streams, and irrespective of any habitat short fallings, the wild native brook trout persist, and even thrive.

The Bad Guys
While habitat is complex and with few absolutes and many exceptions, the issue of nonnative fish is far less complicated. All nonnative fish have at least some negative impacts on wild native fish. At a minimum, nonnative fish compete with native fish for food and space. Nonnative fish can prey on native fish and disrupt spawning. In some cases, nonnative fish can hybridize with native fish. The severity of the impact of nonnative fish depends on the species and their ability to adapt to their new surroundings.
Habitat degradation is absolutely negatively impacting wild native trout in many places. In some cases, it has resulted in their extirpation. And while New England is experiencing more traditional weather than it has over the last decade or so, the long-term trend across the nation has resulted in lower and warmer water, both of which are bad for wild native trout. Floods, droughts, and wildfires have taken their toll as well. And development, resource extraction, and other human uses that are detrimental to wild native trout continue.
What Triggered This Piece
“The team of biologists from across the state caught and visually confirmed multiple largemouth bass of varying ages in the lake. Biologists also confirmed there were no largemouth bass in Orie Lake which feeds into West Musquash, and natural barriers prevent upstream passage of bass into West Musquash, indicating the bass were moved illegally into West Musquash.”
—Ariana St Pierre, WGME
My news feed recently contained a link to an article about the confirmation of nonnative bass, largemouth in this case, in yet another coldwater lake in Maine. Located just north of West Grand Lake, one of just four native-landlocked-salmon lakes in Maine, West Musquash Lake is home to wild native brook trout, wild lake trout of unknown origin, and wild nonnative landlocked salmon. It is also home to one of the few remaining populations of wild native round whitefish in the state. At over 1,600 acres, the lake has a maximum depth of more than 100 feet, so removal of the bass would be impossible.

“West Musquash is a deep, clear, cold-water lake that is truly special to the region and area. The lake supports a wild brook trout, wild lake trout and wild landlocked salmon fishery and also is one of the last waters in the state with a population of round whitefish. This is the only water in the region that has all these fisheries without an active stocking program. Sadly, this introduction will no doubt change the lake forever.”
—Regional Fisheries Biologist Jacob Scoville, Maine Department of Inland Fisheries and Wildlife
Maine is home to more than 650 wild native salmonid lakes and ponds, the most in the nation. This includes brook trout, lake trout, landlocked Atlantic salmon, rare Arctic charr, and lake and round whitefish. Some Maine lakes serve as winter refuge for post-spawn federally endangered sea-run Atlantic salmon. These lakes and ponds are linked to other bodies of water via inlets and outlets, meaning that what impacts one water will most likely impact others, as well.
While Maine has dodged the nonnative fish epidemic to some degree, especially with regard to salmonids, the situation is changing, and dramatically. Brook trout have been eradicated from the St. John River system due to the introduction of nonnative muskellunge. The Belgrade Lakes lost their native brook trout to introduced landlocked salmon, which were negatively impacted by nonnative bass, which are now on the ropes due to nonnative pike.
Nonnative smallmouth and largemouth bass are now common in the Downeast Region of Maine, home to upwards of 90 percent of the nation’s sea-run brook trout, and critical habitat for federally endangered Atlantic salmon. Sebago Lake, the namesake water for landlocked salmon, Salmo salar Sebago, now has nonnative bass, crappie, and pike. Nonnative smallmouth bass are now established in Green, Sebec, and West Grand Lakes, the other three native landlocked salmon lakes in Maine.
Nonnative smelt introductions resulted in Maine having to reclaim two out of twelve remaining native Arctic charr waters. Another native charr water, Bald Mountain Pond in Somerset County, is collapsing under the weight of nonnative lake trout and smelt as we speak. And both nonnative smelt and landlocked salmon can be found in Rainbow Lake, along with the aforementioned bass in Green Lake, all of which are native Arctic charr lakes.
Nonnative smallmouth bass have greatly compromised the fabled Rapid River and are at risk of spreading further into the Rangeley Lakes Region, including the equally famous Kennebago River. Nonnative bass and pike are now at the doorstep of the nearby Magalloway River. Moosehead Lake, the largest wild native brook trout mountain lake in the east, is now home to a fishable population of nonnative smallmouth bass and white perch.
My home river, the Kennebec in central Maine, now has nonnative bass throughout its length, as well as in many tributaries, including the Dead River as far upstream as Grand Falls. And my favorite wild native brook trout pond, Round Pond in West Forks, was lost to an introduction of nonnative golden shiners and fathead minnows a decade ago, in spite of having been closed to the use of live fish as bait for decades.

Brown trout are not native anywhere in North America, and they often outcompete native fishes in waters where browns have been stocked. This fish was caught from a Vermont stream full of native brook trout. Photo: Phil Monahan
The Solution
While nonnative bass, pike, muskies, and walleye get all the attention, at least from trout anglers, historically, more wild native trout have been lost to the introduction of nonnative salmonids. This is rarely discussed in a scientifically sound manner, and when it is, it is often challenged and defended. While trout anglers band together in regard to habitat, we are greatly divided and often silent, or worse complicit, on the subject of nonnative fish, especially trout.
Consider the extensive loss of native cutthroats from the Rocky Mountains, much of which is due to hybridization with nonnative rainbow trout. Native rainbow trout in the West have been greatly compromised as a result of introduced brown trout. And the unique Apache trout and Gila trout of the southwest have been forced to compete with nonnative brown trout and rainbow trout, on top of droughts and wildfires that are outside of our control.
Both Pennsylvania and New York—as well as Vermont, Massachusetts, Connecticut, and Rhode Island to a lesser degree—have lost many of their wild native brook trout populations to nonnative brown trout. Wild nonnative rainbow trout can be found on top of wild native brook trout throughout central and southern Appalachia. And native bass in the south are now being stressed by introduced bass through hybridization.
It’s easy to blame habitat for our native fish woes. It points the gun at someone else, not us. Habitat work deflects the blame on others. Habitat work has many friends and few enemies—with the exception of dam removal—and the enemies it has have few friends.
Conversely, nonnative fish have many friends and far too few enemies. And most of their friends come from within our own ranks, the angling community. While trout anglers rail against the introduction of nonnative warmwater fish, we are dangerously silent with regard to nonnative trout. This needs to change if we are to save what we have left.
“Fish, Fish, Fish” is as incomplete a solution as “Habitat, Habitat, Habitat.” Focusing on one but not the other will not stop the bleeding nor turn the tide. Without an effort to mitigate nonnative fish where they are present, habitat work can result in an increase in nonnative fish not an increase in native fish. While mitigating nonnative fish usually results in an increase in native fish, the ceiling can be limited by insufficient habitat. Imagine what we could accomplish if we addressed both.
BOB MALLARD has fly fished for forty years. He is a former fly shop owner, Registered Maine Fishing Guide, and fly designer. Bob is a blogger, writer, and author. He is also a founding member and Executive Director for Native Fish Coalition. Look for his books 50 Best Places Fly Fishing the Northeast, 25 Best Towns Fly Fishing for Trout, Squaretail: The Definitive Guide to Brook Trout and Where to Find Them, and Favorite Flies for Maine: 50 Patterns from Local Experts. His next book, Fly Fishing Maine: Local Experts on the State’s Best Waters is due out late 2022. Bob can be reached at BobMallard.com or [email protected].