Examining the impacts to Georgian Bay freshwater ecosystems from net pen or cage aquaculture

Expanding net pen (or cage) aquaculture operations in Georgian Bay is being advanced as an opportunity by many levels of government in Canada as well as the industry. Ontario is unique in Great Lakes jurisdictions allowing net pen aquaculture in public water. In 2017, Georgian Bay Forever asked the University of Guelph to compile past freshwater aquaculture research on environmental impacts, and is partnering in 2018 to address gaps with new research that will determine if high density net pen aquaculture poses a threat to the health of the ecosystem. (Last update May 7th, 2018)

Cage Aquaculture

Fish farming in Ontario used to be more land-based. Today, freshwater aquaculture occurs primarily within lakes and is a practice that involves rearing fish in cages suspended in a lake.1 The government awards public water space and therefore free wastewater treatment to the cage industry. Noticeably, there was a shift to 88 percent cage production by 2010 - a good proportion of those happening in or on the borders of Georgian Bay. According to a Department of Fisheries and Oceans Canada (DFO) report2 , in terms of freshwater, “Lake Huron is the site of most cage based aquaculture in Canada”, although no new licences have been issued in Ontario since 2003.

How does aquaculture compare with commercial fisheries in Ontario?

Ontario Trout aquaculture production

In 2014, commercial fisheries caught over 11 thousand tonnes of fish, a decline of more than a half since 1990. Aquaculture has remained flat for the last 15 years with an average of 4 thousand tonnes.3 Industry sees opportunity in net pen (cage) aquaculture and cites Iran as a jurisdiction to model for growth. In Iran, the industry has multiplied rapidly with government support, from 5 thousand tonnes in 1978 to about 375,000 metric tonnes of fish in 2014. However, the Iranian example includes several species including Asian carp, shrimp, saltwater fish, as well as coldwater trout. With limited freshwater and different species, Iranian industry farming is also comprised of several different farming methods, including the use of raceways, ponds, and land-based systems. In addition, those numbers include the fish fry the industry raises to help re-stock depleted fish populations to aid commercial fishing.4 As growth is considered, some important differences arise around diversity of species, location, and methods.

Why is it important for the Georgian Bay Community to be engaged?


In 1973, Experimental Lake 226 in the Kenora District was divided into 2 basins. Extra phosphorus was added to one side by scientists. As a result of this experiment, phosphates were banned from detergents.
Now, extra Phosphorus from open cage aquaculture is a risk to freshwater in Ontario. However, many areas of Georgian Bay are more dynamic than Lake 226. In some areas, Phosphorus nutrients are actually too low to support a healthy aquatic ecosystem.
To mitigate risk, it is critical for GBF to examine impacts from open cage aquaculture within more complex and diverse Georgian Bay sites.
Ecosystem impacts could vary widely — potentially negative in some areas, or positive in others. GBF is at the forefront of finding out these impacts, in order to inform improved regulation. Read on to learn what we’ve discovered so far.
(Photo source Department of Fisheries and Oceans)
Because there are opportunities and risks. On the opportunity side, there is a need for fish protein to meet growing population demands. For Canada and Ontario, governments see potential for the economy in general, and regionally for the North. On the risk side, there are concerns about the impacts to water quality and ecosystems that are critical to shoreline communities.

Currently, Georgian Bay has 5 operators with 7 sites as well as a few unlicensed First Nations operations. The Ontario and Canadian Government seem in general committed to growing the industry, while simultaneously having the power to monitor and regulate the industry to protect the environment for future generations. This internally perceived conflict of interest has created some inertia, impeding their ability to create functional guidelines for cage aquaculture. Some in the industry blame the government for the lack of growth.

Regulatory lull provides opportunity to better understand impacts

Right now, there is a critical opportunity for Georgian Bay Forever to work with partners to provide scientific research into potential interactions to further inform debate around sustainable aquaculture. We will be sharing this information with stakeholders and authorities. It is complex, and there is a range of stances on what “sustainable” means with respect to net pen aquaculture that are ever evolving as stakeholders lobby each other and more research becomes public. Some stances include: banning future net pen aquaculture growth (the Great Lakes Fishery Commission, US advisors)5, another looks to improving regulations around site selection based on areas where more phosphorus inputs may not be problematic. It should be noted that Ontario is alone among Great Lakes jurisdictions in its allowance of open net pen aquaculture.

The DFO is currently investigating the possibility of creating an Aquaculture Act. The Canadian Aquaculture Industry Alliance observes that “The proposed Aquaculture Act represents a step forward in modernizing how Canada views, regulates, and enables growth of our industry. Rather than being regulated under a 150 year old Fisheries Act, the Aquaculture Act would recognize our industry as a farming activity – consistent with the approach of other leading jurisdictions around the world.”6

What has GBF found in past research on cage aquaculture impacts?

GBF is committed to protecting the water and the biodiversity of its aquatic species with evidence based research. In 2017, we continued the partnership with the University of Guelph (U of G) and focussed on the following:

    1. Synthesizing past net pen aquaculture research on freshwater impacts.
    2. Using stable isotopes and fatty acids to determine if native fish were consuming aquaculture feed, with the potential to use DNA barcoding in future research.
    3. Developing research questions and methodologies to fill in the gaps and address concerns to be able to implement a more sustainable policy.


Under commission by GBF, the University of Guelph (U of G) looked at 56 research reference points to produce a summary, Freshwater Aquaculture: A review of the Environmental Implications (09/26/2017). The full report can be found at this link , but it came to the conclusion that “If the net-pen aquaculture industry is to continue and expand in The Great Lakes, there needs to be improvement to policy regarding the establishment of cage aquaculture operation, and a better understanding of how freshwater cage culture affects lake ecosystems is required to meet this objective.”1 The main issues generating environmental concerns fall under these categories:

    Waste production and uptake

    The main concern is nutrient subsidies of primarily phosphorus (in solid or liquid form) augmenting those found in the natural environment. This concern has been partially attenuated by industry through good husbandry practices, but certainly not entirely eliminated.

    The 2 broader fallout concerns are as follows:

    CONCERN 1: Excess phosphorus in the aquatic environment can result in “significant algal blooms and eutrophication”1. Eutrophication starves lakes of oxygen and leads to death of animals in that water body.The good news is that phosphorus loading in aquaculture has been steadily reduced over the years due to changes in the make-up of the feed, and site selection. The feed is a huge expense for the industry, so reducing waste also reduces feed costs. Sites that have more dynamic water circulation and more depth are better than stagnant, enclosed bays. “In general, the reviewed literature supports the view that modern cage farms with good husbandry that are located in well-flushed, deep basins do not show significant, long-term effects on water column nutrient concentrations.”1 CONCERN 2: Human derived subsidies of nutrients (extra feed and fish waste) can be consumed by native species, altering the food web and potentially impacting species health. “This organic material can act as a food source for invertebrate and fish species, and studies have shown that natural fish populations surrounding cage culture operations exhibit a shift in diet towards that of the released cage culture feed and waste (Fernandez-Jover et al., 2007a; Fernandez-Jover et al., 2011).”1

    U of G further notes there have been some studies in small experimental lakes that have shown “increased abundances of benthic organisms, increased growth, reproduction and densities of invertebrates and small fish.”1 However, these cannot be directly applied to more dynamic and larger lakes that are more commonly chosen for aquaculture.


    This is an unresolved issue. The concern with excessive phosphorus (P) is that it is the limiting nutrient in freshwater lakes and can lead to toxic and non-toxic cyanobacteria blooms resulting from eutrophication.

    However, there is a wide range of potential P release from sediments depending on conditions, including one reference noting a 7% to 64% spread.1 The U of G summary noted that “the factors affecting the rate and total proportion of P that is recycled from sediment into the water column have not been well studied in Ontario or with current feed formulations and practices. Since P is the nutrient limiting primary production in lakes, and that the solid waste portion of P is the largest component of P lost to the environment, this knowledge gap significantly hinders our ability to predict the effects of aquaculture activities on lake productivity (Temporetti and Pedrozo, 2000).”1 Providing some needed insight into the complexities around release of phosphorus from sediment is a 2014 study by L.A. Molot et al., entitled “A novel model for cyanobacteria bloom formation: the critical role of anoxia and ferrous iron”7 published in Freshwater Biology that was partially funded by GBF.


    The major argument is that ferrous iron (Fe2+) regulates the ability of cyanobacteria to compete with its eukaryotic [non-toxic algae] competitors due to its increased iron requirements to support photosynthesis among other important environmental considerations. Therefore, cyanobacteria dominance emerges under more specific lake circumstances than previously widely considered. For example, it provides rationale that deep lakes are less susceptible to cyanobacteria bloom. The anoxic zone (low oxygen) is so deep that it falls below the mixing zone where anoxic sediments, Fe2+ and the euphotic zone (where photosynthesis occurs) could interact with cyanobacteria. Inshore regions or shallower lakes could be more prone. Furthermore, the report challenges where anoxia can develop, noting that it is not limited to eutrophic systems.

    In short, GBF believes the Molot paper highlights the need to not look in isolation at P sediment build-up from aquaculture sites, but examine other environmental circumstances and potential management solutions that effect cyanobacteria formulation. (Read the report at this link.)

    In the meantime, there have been some mitigation measures and potential solutions offered that could decrease the accumulation of sediment that contains P. These include: sediment regulations, fallowing, and more efficient feed formulations and technological cage innovations that can capture some of the waste.

    Ecological and genetic interactions that may occur between escapees and indigenous species
    Recent news reports on our ocean shores show that this is a risk. A most recent example is an incident last summer involving a fish farm owned by Cooke Aquaculture Pacific. Pens collapsed under high winds letting up to 263,000 Atlantic salmon escape into the Pacific where they became invasive species with potential consequences for native salmon.9 The same Globe and Mail article notes escapes that have happened on the East Coast resulted in some hybrids that are less capable of survival. According to Globe and Mail source Neville Crabbe of Canada’s Atlantic Salmon Federation, “Wherever the open net pen industry is established on the east coast of North America, the wild salmon populations have plummeted.” While not an exhaustive list of all the factors that could impact native ecosystems and water quality, the above is a summary of issues that were found by the GBF/UofG background research project.

    As noted earlier, for more information, please check the full report.


The University of Guelph's Review of Freshwater Environmental Implications (Laura Johnson and Kevin McCann), commissioned by Georgian Bay Forever. To read the report, click here
In their Spring 2018 newsletter, the Georgian Bay Association recently revealed concerning information obtained under a Freedom of Information and Privacy Protection Act request. The obtained MOECC reports included information that the water quality in Lake Wolsey has deteriorated to below Provincial objectives, and that 45% of the phosphorus input to Lake Wolsey comes from the aquaculture operation.10 This provides further evidence that each site must be really carefully selected and rigorously evaluated; and that more research needs to be done on the criteria that makes a site sustainable.

cyanobacteria research

The academic article, A novel model for cyanobacteria bloom formation: the critical role of anoxia and ferrous iron (Molot, and others) that GBF partially funded, was cited by the Department of Fisheries and Oceans (DFO) in a 2017 report Freshwater Cage Aquaculture: Ecosystems Impacts from Dissolved and Particulate Waste Phosphorus.2

GBF won’t stop looking for gaps and supporting research that lead to more informed decisions. Read on to see our next research questions on this topic.

2017 GBF commissioned research produces proof of food web interference.

GBF’s partner U of G conducted a research project using stable isotope and fatty acid bio-tracers (information from the tissue of fish) to determine if aquaculture waste was being consumed by species in the natural environment in Parry Sound.

It is. The research found that pelagic or offshore native fishes, both an intermediate consumer (cisco) and a top predator (lake trout), were consuming the excess feed. Furthermore, the project also found that these fish had higher n-3 fatty acids levels in their tissue in comparison to other Lake Huron sites. These n-3 fatty acids have been shown to impact fish health by increasing survival and reproductive success.

These results indicate more research needs to be done on aquaculture waste and its interaction with natural species.

aquaculture update

An update from the University of Guelph on their new research (May 2018) on cage aquaculture

GBF won’t stop looking for gaps and supporting research that lead to more informed decisions. Read on to see our next research questions on this topic.

New research will fill gaps and lead to more informed sustainable policy.

The 2017 GBF commissioned research project and its background compilation of freshwater research, as well as relevant Lake Wolsey disclosures, have clarified these research needs that GBF and U of G will be tackling in 2018.

The big questions GBF must tackle next

  • What are the impacts to local ecosystem structure and function, particularly local native fish populations?

  • How do the human derived subsidies of excess feed and faecal matter impact the food web in Georgian Bay aquaculture locations?

  • How do the effects of aquaculture vary among sites that differ in placement (e.g. depth and exposure) and management practices (e.g. feeding regimes)?
To help answer those bigger questions, here is a breakdown listing of the individual projects.

Using stable isotopes and fatty acids analysis in Parry Sound vs. other regions of L. Huron, the project will examine if top predators like lake trout, walleye, and small mouth bass are consuming waste and feed from cage operations. This biotracer approach will be carried out in concert with SONOR surveys around cages to quantify the abundance and distribution of predators around net pen areas.

These species are good bio-indicators of ecosystem health. Researchers will be looking at the difference in macroinvertebrate composition (ie. what species are present) between aquaculture sites vs. control sites in L. Huron to see if there is a difference in species diversity due to aquaculture waste input.

While this practice is a recommended husbandry technique to mitigate sediment build-up, the impacts on the individual fallowing areas chosen need to be understood to see if further adjustments need to be made (i.e. choosing an appropriate site to fallow to reduce environmental impacts).

And does it vary by location of aquaculture? Lake Trout is a model species for monitoring cumulative effects such as habitat degradation, contaminant load, changes in food web structure, and eutrophication because their health and physiology reflect changes in the environment. Lake trout liver size (a metric of contaminant load), gonad (a measure of reproductive potential), stomach (feeding success), muscle tissue samples (biotracers), and brain size (foraging strategy) will be compared between aquaculture sites and control sites. Using lake trout as ‘multi-meters’ of cumulative stress will provide novel and important insights into the effects of aquaculture on the surrounding environment.

GBF is also raising money to support the purchase of an autonomous underwater vehicle that could rapidly and efficiently measure dissolved oxygen, chlorophyll, and pH levels that are concerns.

Major stakeholders have stated an interest in developing a sustainable industry. GBF strongly believes that sustainability policy should be steered by scientific evidence based on research collaboration. Georgian Bay Forever will be following other important research, actions, and policy initiatives of stakeholders, while actively working with U of G to bring forth the answers to the identified research questions that can inform better regulatory decision-making.

We can’t stop now!

There are significant gaps of information that are needed to help decision makers form and implement sustainable policy. Georgian Bay Forever is working with the University of Guelph to answer some important and concerning questions regarding cage aquaculture implications for aquatic ecosystems.

Thank you for your valuable support. Please continue or consider donating to Georgian Bay Forever to support the continuation of projects like these.

Georgian Bay Forever is a charity that funds and supports scientific research, projects and education that protect and enhance the waters of Georgian Bay, as part of the Great Lakes. Our vision is that Georgian Bay waters are healthy and thriving for future generations. Learn more about how you can support out work.
References, sources, and acknowledgements:

Thank-you to all the sources and references in this post.

Note - We try to bring together information to help understand aquaculture. We do use sources to provide information and visuals. We do our best to attribute properly and try very hard to get it right. If we have made an inadvertent mistake around recognizing someone’s work or misinterpreting the work, please let us know via email at communications and we will correct.

1Johnson, Laura and McCann. Kevin. (2017) Freshwater Aquaculture: A Review of the Environmental Implications 9/26/2017. Specific quotes page 2, 11, 8, 5, Fernandez-Jover reference and quote page 10, Temporetti and Pedrozo, reference and quote on page 9, page 10, page 9 (7-64%), Temporetti and Pedrozo second reference page 9
2Otu, M.K., Bureau, D.P., and Podemski, C.L. 2017. Freshwater Cage Aquaculture: Ecosystems Impacts from Dissolved and Particulate Waste Phosphorus. DFO Can. Sci. Advis. Sec. Res. Doc. 2017/059. v + 55 p., page 11 quote, page 13 map, quote page 41
3McGrath, John Michael. (May 2, 2016) New Rules may bring Ontario first new fish farms in 20 years. TVO. Retrieved April 10 at https://tvo.org/article/current-affairs/the-food-chain/new-rules-may-bring-ontario-first-new-fish-farms-in-20-years (citing University of Guelph Figures)
4Powerpoint presentation: Aquaculture in Iran. Prepared by NordOest. Innovation Norway representative in the GCC Region. Sept 2016. Retrieved April 10, 2018 at http://www.akvarena.no/uploads/Ekstern%20informasjon/Aquaculture%20in%20Iran-Market%20introduction.pdf 5The Committee of US Advisors for the US Great Lakes Fishery Commission in 2016 resolved the following: “Be it therefore resolved, the U.S. Advisors to the Great Lakes Fishery Commission call on the Great Lakes Fishery Commission to encourage all Great Lakes jurisdictions to prohibit the establishment of any net pen aquaculture facilities in the U.S. waters of the Great Lakes to protect the water quality and fishery of the Great lakes system.” Retrieved at http://www.glfc.org/pubs/pdfs/resol2016_4.pdf on April 2, 2018.
6Canadian Aquaculture Industry Alliance. Retrieved April 10 from website page http://www.aquaculture.ca/a-new-aquaculture-act-in-canada-index/
7L. A. Molot, S. B. Watson, I. F. Creed, C. G. Trick, S. K. Mccabe, M. J. Verschoor, R. J. Sorichetti, C. Powe, J. J. Venkiteswaran and S. L. Schiff. A novel model for cyanobacteria bloom formation: the critical role of anoxia and ferrous iron. Freshwater Biology. (2014), 59,1323–1340. doi:10.1111/fwb.12334. copyright 2014 John Wiley & Sons Ltd, Freshwater Biology, 59,1323–1340, additional quote page 8 of the PDF or (59 of Freshwater biology)
8Douglas P Connelly, National Oceanography Centre, Southampton in response to a question on research gate. Retrieved on March 23rd, 2018 at https://www.researchgate.net/post/Oxic_and_anoxic_marine_sediments_what_factors_control_this_variability
9Dean Rutz/AP. Washington’s ban on net-pen fish farms has Canadian consequences, salmon group says. The Globe and Mail. March 4th, retrieved March 21, 2018 at https://www.theglobeandmail.com/news/national/washingtons-ban-on-net-pen-fish-farms-has-canadian-consequences-salmon-group-says/article38200537/
10Duncanson, Bob. “GBA Presses Minister for Action on Aquaculture”. from the GBA Update. Vol. 28 no1, Spring 2018.