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Threats to fish and fish habitat

Aquatic ecosystems face numerous threats, from human activities in or near water, land use in the broader watershed, and even natural events. The fish and fish habitat protection policy statement 2019 lists the following broad threats that threaten the health and sustainability of fish and their habitat:

Habitat modification or degradation

Did you know?

Habitat fragmentation is a form of degradation as it separates the habitat into isolated parts. This can disrupt or prevent fish passage to areas of the habitat that provide food and shelter for the species.

Habitat modification refers to changes to the function of an aquatic ecosystem that makes it less suitable to support fish and other aquatic species. For example, the alteration of flow in a watercourse by a dam, water diversion, stream crossings or water extraction can result in negative effects on spawning or rearing, or the death of fish. The loss or degradation of habitat may result from activities like infilling lakes, streams, or wetlands to create dry land or creating barriers to fish passage (i.e., disrupting the connectivity of fish habitat).

Aquatic invasive species

Aquatic invasive species are fish, invertebrate or plant species that have been introduced into a new aquatic environment, outside of their natural range. Canada has numerous AIS, in both freshwater and marine ecosystems. Canada’s federal Aquatic Invasive Species Regulations list over 164 aquatic species as invasive. Some of the more visible freshwater invaders in Canada include Asian carp, sea lamprey, and zebra mussels.

AIS can be introduced accidentally or intentionally in Canadian waters through several pathways such as:

With few or no natural predators, AIS can outcompete native species for food and space. They can degrade habitat by affecting water quality, and by transporting diseases or parasites.

Economic impacts of AIS include:

Overexploitation of fish

Overexploitation of fish, or overfishing, refers to catching amounts of fish that are not sustainable, i.e. fishing at a rate that hampers the ability of the remaining population to rebuild or recover to healthy levels. The depletion of fish stocks can lead to severe economic consequences and alter entire food webs.

Other ways that fishing can lead to depleted and vulnerable fish stocks is through:


Pollution can enter freshwater habitats from a wide range of sources, including but not limited to:

These inputs can harm fish and aquatic ecosystems in many ways. For example, phosphorus is a nutrient that occurs in nature, as well as in human-made products, such as fertilizer and detergent. On its own, phosphorus helps to nourish life in the lake, but when we add to that natural load, phosphorus over-feeds the lake, causing algae and aquatic plant populations to explode, a process called eutrophication (or nutrient enrichment). This can block the sunlight from reaching water depths below the surface, deplete oxygen levels and change species composition and biodiversity.

Climate change

Climate change refers to long-term shifts in temperatures and weather patterns, caused by human activities, especially the burning of fossil fuels.

Canada’s Changing Climate Report (2019), led by Environment and Climate Change Canada and part of Canada’s national assessment process, provides a comprehensive summary of current knowledge about how and why Canada’s climate has changed, and what changes are projected for the future. Some key findings show that:

What does this mean for fish and their habitats?

Increased acidity (acidification) can reduce the availability of carbonate ions (required by some organisms to build shells and skeletal structures) and increase solubility of existing calcified structures. This can translate to reduced numbers of shellfish and impaired health of shellfish and corals. Acidification can also make certain habitats unsuitable for different life stages of organisms and increase algal blooms.

Decreases in dissolved oxygen and nutrient availability can limit biological productivity in surface and subsurface waters and impair respiration of aquatic organisms. Likewise, decreased nutrient availability can impair the growth of aquatic organisms, including those that form the basis of food webs.

Increased precipitation and subsequent runoff have been linked with excess nutrients in water systems, increasing the incidence of harmful algae blooms.

Extreme storm events and flooding can increase runoff of contaminants from the landscape and erode coastlines and shorelines to increase sediment loads in water systems, degrading water quality.

Changes in patterns of precipitation and warmer temperatures mean drought conditions may become more common. For some water bodies, less water flows in rivers or water volume in lakes means that the water heats up quickly in hot summer conditions. Native species that have evolved to occupy these habitats may no longer be able to tolerate higher temperatures, and their traditional food sources may become limited or disappear.

DFO’s State of Canadian Pacific salmon report explains how climate change effects to marine and freshwater ecosystems are impacting Pacific salmon at every stage of their life cycle.

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