Invasive Species That Are Changing Ontario Waterways
In the late 1980s, a cargo ship discharged its ballast water into Lake St. Clair, and with it came the larvae of a small, striped bivalve from the Black Sea. Within a decade, zebra mussels had colonized every corner of the Great Lakes, encrusting water intake pipes, smothering native mussel beds, and fundamentally altering the food web of the largest freshwater system on Earth. It was one of the most consequential biological invasions in North American history, and it was only the beginning.
Ontario's waterways are now home to dozens of non-native species that arrived through shipping ballast, the aquarium trade, bait bucket releases, and deliberate introductions gone wrong. Some have faded into the background, establishing small populations that coexist uneasily with native species. Others have reshaped entire ecosystems, altering water chemistry, displacing native wildlife, and costing the province hundreds of millions of dollars in economic damage.
Zebra and Quagga Mussels: The Filter Feeders
Zebra mussels and their close relative, the quagga mussel, remain the most impactful aquatic invaders in the Great Lakes. A single adult mussel can filter a litre of water per day. Multiply that by the trillions of mussels now blanketing the lake bottoms, and the cumulative effect is staggering. The mussels have filtered the water of the Great Lakes to an unnatural clarity, which sounds beneficial until you understand what it means ecologically.
Clearer water allows sunlight to penetrate deeper, fuelling the growth of bottom-dwelling algae, including the filamentous green algae Cladophora, which washes ashore in reeking mats every summer along beaches from Cobourg to Kincardine. The mussels also concentrate nutrients on the lake bed, redirecting energy away from the open-water food web that supports species like alewife, smelt, and the lake trout that feed on them.
On a practical level, the mussels clog water intake pipes for municipal water systems and industrial facilities. The estimated cost of mussel-related maintenance across the Great Lakes basin exceeds $500 million per year. In Ontario, even small lakefront communities with modest water systems have had to install filtration screens and chemical treatment to keep mussel larvae out of their infrastructure.
Phragmites: The March of the Common Reed
If you have driven along a highway near Lake Huron, Georgian Bay, or Lake Erie in the past decade, you have seen phragmites. The European common reed, Phragmites australis subsp. australis, forms dense stands up to five metres tall that crowd out every other plant species in their path. It spreads through underground rhizomes that can extend ten metres or more from the parent plant, and a single stand can produce millions of seeds per year.
Phragmites has devastated coastal wetlands across Ontario. Where diverse communities of cattails, bulrushes, sedges, and native grasses once supported a rich web of birds, amphibians, and insects, phragmites creates a biological desert. The dense canopy shades out understory vegetation. The thick litter layer suppresses seed germination. And the habitat structure it creates is unsuitable for most native wildlife species.
The Ontario government has classified invasive phragmites as a restricted species under the Invasive Species Act, making it illegal to import, deposit, release, or propagate the plant. But enforcement is difficult when the species is already present across thousands of hectares. Control programs typically involve herbicide application (glyphosate sprayed in late summer), followed by cutting and burning. The work is expensive, labour-intensive, and must be repeated over multiple years to exhaust the root system. For more on the broader wetland implications, see our piece on the quiet disappearance of coastal wetlands in Ontario.
Round Goby: The Bottom Dweller
The round goby, a small bottom-feeding fish native to the Black and Caspian Seas, arrived in the Great Lakes in the early 1990s through ballast water. It is now the most abundant fish species in the nearshore zone of all five Great Lakes. Gobies are aggressive competitors for food and spawning habitat, and they prey directly on the eggs and fry of native species including smallmouth bass, walleye, and lake sturgeon.
The goby's impact on native fish populations has been especially pronounced in rocky nearshore areas, which are critical spawning habitat for several commercially and recreationally important species. Our reporting on what happens to fish habitat when shorelines get developed explores how the combination of invasive species and physical habitat loss creates compounding pressure on native fish.
There is one ecological silver lining. Gobies have become a significant prey item for larger predators including smallmouth bass, lake trout, and double-crested cormorants. Some researchers argue that the goby has become integrated into the food web to the point where removing it, if that were even possible, would now cause as much disruption as its arrival did.
Sea Lamprey: The Original Invader
Long before zebra mussels, the sea lamprey nearly destroyed the Great Lakes commercial fishery. This parasitic eel-like fish, native to the Atlantic Ocean, gained access to the upper Great Lakes through the Welland Canal in the early twentieth century. By the 1940s, it had devastated populations of lake trout, whitefish, and burbot across Lakes Huron, Michigan, and Superior.
The binational Great Lakes Fishery Commission has been managing sea lamprey since the 1950s, using a combination of chemical lampricide treatments in spawning streams and physical barriers to block upstream migration. The program has reduced lamprey populations by approximately 90 percent from their peak, and it remains one of the most successful invasive species management efforts in the world. But it requires continuous funding and effort. If treatments were halted, lamprey populations would rebound within a few years.
Asian Carp: The Looming Threat
Bighead and silver carp, collectively referred to as Asian carp, have been advancing up the Mississippi River system toward the Great Lakes for two decades. These large, fast-growing filter feeders consume massive quantities of plankton, directly competing with native fish for the base of the food web. Silver carp are also notorious for leaping out of the water when disturbed by boat motors, posing a genuine safety hazard to boaters.
The U.S. Army Corps of Engineers has been constructing a barrier system at the Brandon Road Lock and Dam in Illinois, designed to prevent the carp from reaching Lake Michigan. On the Canadian side, the Department of Fisheries and Oceans has developed an early detection monitoring program in Lake Erie and Lake Ontario. Individual grass carp, a related species, have already been caught in Ontario waters, but there is no evidence of an established breeding population yet.
What Can Be Done
The uncomfortable truth about aquatic invasive species is that once they are established, eradication is almost never possible. Management focuses on containment, population suppression, and preventing new introductions. Ontario's Clean Equipment Protocol, which requires boaters and anglers to clean, drain, and dry their equipment between water bodies, is one of the most important frontline defences against spreading existing invaders to new lakes.
For waterfront property owners, understanding which invasive species are present on their lake and taking steps to avoid inadvertently helping them spread is a practical starting point. That means never dumping aquarium contents into natural water bodies, never moving bait fish between lakes, and reporting sightings of new or unusual species to the Ontario Invasive Species Hotline.
Some of the most promising restoration work happening today combines invasive species control with broader shoreline restoration efforts, tackling the physical and biological damage simultaneously. It is painstaking work. But for the waterways that define Ontario's landscape and identity, it is essential.
