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Nonpoint source pollution

Point sources of contamination in the waters of the St. Lawrence, such as municipal and industrial effluents, are fairly well characterized and localized. On the other hand, nutrients and various contaminants from the agricultural areas cause nonpoint source pollution, which is at the origin of eutrophication and contamination problems in the waters of the St. Lawrence. Research of new solutions to reduce the sources and impacts of nonpoint pollution is necessary.

Projects 2021-2026

Develop a project to assess the environmental risks attributable to various sources of contamination in the Quebec City area

Human activity along the St. Lawrence River in the Quebec City area is likely to have an impact on water and sediment quality. The main causes are municipal wastewater effluent discharged by various municipalities, including Quebec City and Lévis, as well as wastewater treatment plant effluent discharged by several industries in the region into the river. There are also many port facilities and marinas in the region in which contaminated sediments are likely to accumulate. Lastly, inputs of agricultural contaminants to some of the tributary watersheds of the river must also be considered.

The project consists of three phases:
1- Provide an overall picture of the risk associated with the sources of contamination present in the Quebec City region.
2- Evaluate the presence of contaminants in water and sediments in the Quebec City region and their effects on aquatic and piscivorous wildlife species , and identify the riparian areas where contaminated sediments are most likely to accumulate.
3- Conduct an ecotoxicological risk assessment that can lead to management measures.

Evaluate the effectiveness of retention ponds in improving water quality in agricultural watersheds

Retention ponds retain suspended solids, immobilize nutrients, and degrade pesticides carried by runoff from agricultural fields. The filtering and treatment capacity of retention ponds is due to residence time and settling. The ponds are therefore a possible solution for water treatment and could reduce the impact of nonpoint source pollution from agricultural runoff on the St. Lawrence ecosystem.

In the 2021-2026 phase, the project will address the changing hydrological regime, which is characterized by a marked decrease in precipitation. In the context of a changing climate, retention ponds could also provide an alternative source of water for crop irrigation during drier summer periods. However, it will be important to evaluate the toxicity of the water and sediments applied to the soil.

The project will provide a chemical characterization of the water and sediment in the pond (nutrients, pesticides, etc.) and assess the ecotoxicological risk associated with their recycling to terrestrial organisms in agricultural soils.

Evolution of seagrass beds in the St. Lawrence

Aquatic plant communities provide an essential ecosystem for the health of the St. Lawrence. They provide critical feeding habitat, refuge and physical structure that supports  invertebrates, fish, amphibians, reptiles and aquatic birds. These environments are constantly evolving and are under pressure. Climate change could exacerbate the existing pressures on aquatic plant communities from agriculture, shoreline urbanization or encroachment on the littoral zone. At present, we have only a partial picture of the temporal evolution of the distribution, abundance and taxonomic composition of the river’s aquatic plant communities.

The creation of a working group on St. Lawrence meadows will make it possible to coordinate the acquisition of knowledge on the distribution of aquatic plants in several sectors of the river. Several projects that have been developed in the past, also related to aquatic plant communities, are currently underway. However, the current status of the aquatic plant communities in the fluvial section and estuary must be assessed in order to be able to coordinate all actions, target areas with high potential for such environments and increase the capacity to act on certain factors. The main objective of the project is to ensure that all stakeholders involved in aquatic grass beds are aware of existing and future actions.

Assess the presence and effects of pesticides on aquatic organisms

The presence of various herbicides in the tributaries of Lake Saint-Pierre has already been documented. These tributaries drain agricultural land planted primarily to corn and soybeans. The most commonly detected herbicides in the tributaries are S-metolachlor, glyphosate, atrazine, dicamba and bentazone. The presence of neonicotinoid insecticides has also been reported at concentrations that sometimes exceed the established criterion for the protection of aquatic life.

This observation led to the implementation of key initiatives to bring more environmentally friendly agricultural practices to the Lake Saint-Pierre shoreline and its entire watershed.

The objective of the project is therefore to document the effectiveness of new agricultural practices that have been adopted to improve the quality of aquatic ecosystems. Scientists have designed environmental monitoring approaches that include measuring pesticides in water at different times of the year. At the same time, the potential effects of pesticides on biological responses of various aquatic organisms (e.g., algae, invertebrates and fish) will be assessed. The results of these studies will provide us with a better understanding of the effects of agricultural activities on aquatic communities and enable us to document the impact of new practices on water quality in order to help manage this unique ecosystem.

Effects of agricultural toxins in Lake Saint-Pierre

Organisms in aquatic ecosystems are constantly exposed to complex combinations of natural and chemical stressors. The presence of nutrients and pesticides from intensive agricultural activities in streams, coupled with longer summers and rising water temperatures, can cause stream eutrophication. Eutrophication may lead to increased cyanobacteria populations, some of which can produce toxins. In addition, pesticides can affect aquatic organisms and even promote the development of more resistant and harmful algal species. These sources of stress to the aquatic environment are generally studied individually. Understanding the complex pattern of interactive effects of cyanobacteria and pesticides, and gaining new knowledge on this subject, is important in determining the extent of this issue for Lake Saint-Pierre. 

In this context, this St. Lawrence Action Plan project aims to carry out an exploratory study of the risks associated with the presence of cyanobacteria coupled with that of new families of pesticides to freshwater aquatic organisms and to measure the risks for the aquatic environment. These results will then be used to define subsequent knowledge acquisition needs for these substances.

Evaluate health risks of potential swimming sites in the river

Many sites along the banks of the St. Lawrence River are used for various recreational activities, including water sports (swimming, canoeing, windsurfing, etc.). Some of these sites are part of the Environnement-Plage program or undergo regular water quality monitoring, while others are not officially monitored for bacteriological quality.

Many users want to enjoy the water at official and unofficial swimming spots along the river. In this context, the identification of potential sources of pathogens that pose a health risk using indicators of fecal contamination is becoming an issue. On the one hand, it is important to be able to inform the public more quickly about the risks involved. On the other hand, it is necessary to understand the risks related to the potential presence and origin of pathogens.

The program of the Quebec Ministère de l’Environnement et de la Lutte contre les changements climatiques for monitoring bacteriological water quality along the banks of the St. Lawrence River already collects data at 16 sentinel sites between Montreal and Quebec City. The sites visited for this follow-up will be the subject of additional sampling. The data collected will be used to evaluate a more rapid method of detecting E. coli, to identify potential sources and to determine the presence of antibiotic resistance.

Implementation of the Agriculture Consultation Committee

The implementation of the Agriculture Coordination Committee’s action plan under the St. Lawrence Action Plan is intended to coordinate the actions carried out in the agricultural community. These actions will contribute to improving the quality of the water of the St. Lawrence and its tributaries.

One of the main objectives of the committee is to harmonize the interventions of programs and organizations in and around the Lake Saint-Pierre watershed priority area. Initiatives specific to Lake Saint-Pierre include Agriculture and Agri-Food Canada’s Living Labs, the Pôle d'expertise multidisciplinaire en gestion durable and the Cohabitation agriculture-faune project.

Projects 2016-2021

Mapping of water masses in Lake Saint-Pierre to support water quality monitoring

Lake Saint-Pierre, a widening of the river upstream from Trois-Rivières, supports a rich biodiversity. It is on the List of Wetlands of International Importance (Ramsar List) and is part of UNESCO’s terrestrial biosphere reserves. However, it receives a large number of agricultural contaminants, including pesticides.

For this project, our scientists are using hydrodynamic modeling to provide daily mapping of the water masses that make up Lake Saint-Pierre according to the average hydrological conditions of the previous 24 hours. The mapping provided is therefore representative of the flow and water quality contributions from each of the Lake Saint-Pierre outlets. The maps support water quality monitoring in three ways:

  • By locating the areas most likely to be affected by contaminants from agricultural sources;
  • By determining the area of influence of each outlet;
  • By allowing sampling plans to be adapted following a review of the location of data collection sites.

Evaluate the effectiveness of retention ponds in improving water quality in agricultural watersheds

Streams flowing into Lake Saint-Pierre often contain pesticides, nutrients (nitrogen and phosphorus) and suspended solids that can harm aquatic life. A large proportion of these pollutants come from agricultural operations located within the lake’s watershed. It is believed, however, that the use of retention ponds could mitigate the impact of agricultural nonpoint source pollution. External linkWhen water slows down as it passes through a retention pond, pesticides and nutrients settle out and are retained by the pond. They can then be degraded or immobilized by contact with plants and microorganisms. A retention pond could therefore reduce contaminants in surface water and agricultural drainage.

For this project, our scientists are evaluating the effectiveness of such retention ponds. The results show that the studied pond represents an efficient solution to retain nutrients, TSS and some pesticides (glyphosate and its degradation product AMPA as well as thiamethoxam). However, the pond water had toxic effects on algae growth and American toad development. In addition, the pond created conditions favourable to greenhouse gas (GHG) production.

Better understand the pathogenic microorganisms in the Lake Saint-Pierre watershed

Runoff carries microorganisms into Lake Saint-Pierre that are potentially harmful to humans and wildlife. Indeed, in the first phase of SLAP, our scientists observed high levels of E. coli in the tributary streams of the lake, indicating fecal contamination and the potential presence of pathogenic microorganisms . They also found that these indicator bacteria were resistant to several antibiotics. In addition, Giardia and Cryptosporidium parasites and Campylobacter bacteria were measured in raw water from four drinking water intakes.


Our scientists are evaluating these types of pollution and have presented the results of measurements of fecal contamination indicator bacteria and pathogenic microorganisms identified in these streams at different locations.


Ministry of Sustainable Development, Environment and Climate Change. 2016. Bilan de la qualité de l'eau potable au Québec 20102014. 80 p. http:External link// link ( in French only). 

Villemur R., M. Imbeau, M.N. Vuong, L. Masson, and P. Payment (2015). An environmental survey of surface waters using mitochondrial DNA from human, bovine and porcine origin as fecal source tracking markers. Water Research, 69, 143-153. External

Evolution of Lake Saint-Pierre’s aquatic-grass beds

The aquatic plant communities of Lake Saint-Pierre provide essential habitat for fish, amphibians and waterfowl. Aquatic plants act as a physical structure that supports the algae and crustaceans on which vertebrates feed, and provide refuge from predators. However, little is known about the distribution of the plants that make up these beds or how they evolve over time depending on the quantity (depth and current) and quality (transparency and nutrients) of the water.


Our scientists produce a portrait of the grass beds in Lake Saint-Pierre and the biomass of aquatic plants and algae in order to characterize the habitat available to the fish and invertebrates that inhabit it. By monitoring the beds for several years and considering the evolution of the abundance of various plants, they can assess the factors that influence their health and determine their sensitivity to climate change.

Prepare and hold an exchange workshop on Lake Saint-Pierre

Multiple factors have contributed to the degradation of the littoral habitats of Lake Saint-Pierre and the major ecosystem changes that have been observed in recent years. These include agricultural activities in the floodplain, significant interannual variability in water levels due to climate change, and the presence of pesticides and nutrients in the lake waters.

The purpose of this project is to bring together experts involved in research and action on Lake Saint-Pierre in a workshop to discuss the knowledge acquired and past and future actions. These exchanges will allow us to take stock of knowledge gaps that need to be addressed, as well as the actions to be taken to ensure the integrity of this unique ecosystem.

Exchange workshop on Lake Saint-Pierre 2019 - Summary

Assess the effects of pesticides on aquatic organisms

Intensive agriculture in areas such as Lake Saint-Pierre is one of the causes of the degradation of the aquatic environment. Little is known about the effects of pesticides present in sectors bordering the river or carried by tributaries on the aquatic fish and wildlife of Lake Saint-Pierre. However, we do know that these tributaries drain agricultural lands where corn and soybeans are the predominant crops and that the herbicides most commonly used on these crops, S-metolachlor, glyphosate and atrazine, are detected in Lake Saint-Pierre and in the rivers that flow into it. More recently, the presence of neonicotinoid-type insecticides has also been reported. The combined presence of herbicides and insecticides can therefore affect the aquatic wildlife of this sector.

In this project, our scientists are assessing the biological effects on aquatic organisms of exposure to agricultural pesticides in the St. Lawrence watershed, and particularly on aquatic organisms that occur in Lake Saint-Pierre. The study determines the concentration of various pesticides in the water and measures their effects on aquatic organisms, such as yellow perch and invertebrates, exposed in the natural environment or in the laboratory.

Projects 2011-2016

Richelieu's "Corridor Vert et Bleu"

The Richelieu River is a jewel of biodiversity. It is home to a number of species in precarious situations, among them the copper redhorse. However, urban development and agricultural practices pose major challenges in terms of improving the river’s water quality and habitats. Moreover, the sediment and pollutants observed in the Richelieu flow into Lake Saint-Pierre. One-time restoration measures along the shorelines in this watershed are not sufficient for maintaining adequate water quality, and the participants and collaborators in the St. Lawrence Action Plan seek to implement a comprehensive conservation and restoration project. This initiative will make it possible to conserve a riparian strip to reduce water pollution and create an ecological corridor, install sedimentation systems in ditches and preserve, restore and connect natural spaces throughout the watershed area.

Read the explanatory brochure for the project.

Read the backgrounder for this project.

Develop agricultural water courses on the coastline in the lake Saint-Pierre flood plain

A significant portion of the Lake Saint-Pierre shoreline is used for agricultural purposes, with large blocks of land being gradually converted for large-scale farming, which reduces the substrate of plant material available in the spring for fish habitats. Several participants and collaborators have partnered to develop an approach for restoring these fish habitats. Seven watercourses have been restored since 2003, and this initiative will remain ongoing at a rate of one watercourse per year through 2016 to continue raising the profile of the Lake Saint-Pierre region in terms of sustainable agriculture.

Read the backgrounder for this project.

Continue the activities of the Agriculture Coordination Committee

The objective of this project is to foster increased collaboration among the leading stakeholders in the agriculture sector to establish a common vision of the environmental issues relating to the water quality of the St. Lawrence and its tributaries and to define solutions for protecting these aquatic ecosystems from an integrated management perspective.

Document riverine inputs of organic carbon and nutrients into the marine estuary in relation to hypoxia and acidification

An increase in riverine inputs of organic carbon and nutrients associated with human activities could lead to a eutrophication phenomenon in estuaries and coastal areas. This eutrophication can cause the proliferation of toxic or otherwise harmful algae and the development of hypoxic or acidified zones potentially threatening the health of the St. Lawrence. Documenting the sources and historical evolution of inputs of nutrients and organic matter and the effects of an increase in these inputs, along with the development of numerical prediction tools, will help add to knowledge in this area and support better prediction of these phenomena frequently linked to nonpoint agricultural pollution sources. 

Read the backgrounder for this project.

Improve knowledge about pathogenic organisms from agricultural sources found in tributaries of Lake Saint-Pierre

Livestock manure, cultivated fields and storage areas (manure piles and exercise yards) can contain pathogenic organisms that, on reaching waterways through runoff or agricultural drains, pose a risk to animals and people. In light of the fact that the fecal coliform concentrations measured in tributaries of Lake Saint-Pierre point to the potential presence of pathogenic bacteria, the partners and collaborators seek to gain a better understanding of the risk of water contamination caused by these pathogenic organisms by examining their links to agriculture and providing new information that may assist in decreasing this type of contamination at the source.

Read the backgrounder for this project.

Use the effects of harmful and toxic algae as indicators for monitoring the quality and eutrophication of the water

The proliferation of harmful and toxic algae in the St. Lawrence ecosystem constitutes a growing problem, the effects of which are not yet fully understood. The development of expertise will help provide a clearer understanding of the influence of these algae on the ecosystems in which they proliferate, whether in terms of identifying toxic algae, documenting the factors associated with their bloom and the production and spread of toxins or developing biomarkers and bioindicators. Adding to knowledge about these phenomena will enable the development of prediction tools for sectors at risk and the ecosystem components known to be sensitive to harmful and toxic algae.

Read the backgrounder for this project.