Funding for restoring Great Lakes areas of concern

The application submission period for funding under the Great Lakes Freshwater Ecosystem Initiative is now closed. Please contact us by email at for more information.

The Great Lakes Freshwater Ecosystem Initiative

The goal of the Great Lakes Freshwater Ecosystem Initiative (FEI) is to target the most significant environmental challenges affecting Great Lakes water quality and ecosystem health by delivering on Canada’s commitments under the Canada-United States Great Lakes Water Quality Agreement (GLWQA). The Initiative focuses on the following priority areas for action:

  • restoring water quality and ecosystem health in Great Lakes Areas of Concern (AOCs)
  • preventing toxic and nuisance algae
  • restoring and protecting critically important coastal areas, including wetlands
  • reducing releases of harmful chemicals
  • supporting community-based science
  • increasing participation of Indigenous Peoples in governance, stewardship, and monitoring
  • advancing Great Lakes governance, accountability, and reporting mechanisms

To assist in achieving this goal, the Great Lakes FEI supports action by others to:

  • restore AOCs: Supporting action at the local level to restore water quality and aquatic ecosystem health by implementing projects identified in AOC Remedial Action Plans (RAPs).
  • prevent toxic and nuisance algae: Supporting on-the-ground actions following the Precision Conservation approach, targeting implementation of phosphorus load reduction measures in critical sources areas for nutrient loss, as well as increasing participation in the application of phosphorus load reduction measures by demonstrating innovative approaches and best management practices, and filling knowledge gaps through research and science.
  • restore and protect critically important coastal areas, including wetlands: Supporting and promoting local-level action to enhance water quality, ecosystem health, and the resilience of coastal areas experiencing stress due to climate risks and impacts.
  • reduce releases of harmful chemicals: Increasing participation in the application of beyond-compliance measures to reduce releases of chemicals of mutual concern (CMCs) by developing, implementing, assessing, and promoting use of innovative approaches, as well as enhancing understanding of emerging contaminants that could become CMCs and their potential impacts to the Great Lakes ecosystem.
  • support community-based science: Promoting public engagement in Great Lakes protection through community-based science projects, including advancing stakeholder and public knowledge, improving the sharing and quality of data produced, and advancing broader application of new technologies.
Context: restoring Areas of Concern

Areas of Concern (AOCs) are specific locations designated by Canada and the U.S. under the 1987 GLWQA where water quality and ecosystem health have been severely degraded by human activity at the local level resulting in a range of issues (e.g., beach closures, loss of habitat for fish and wildlife, negative effects on fish and wildlife populations, restrictions on fish consumption, effects on drinking water). Restoring AOCs contributes to the improvement of Great Lakes water quality and ecosystem health as well as the environmental, economic and social wellbeing of local communities in the basin.


An objective of the Great Lakes FEI is to restore the water quality and aquatic ecosystem health of Canadian Great Lakes AOCs. To assist in achieving this objective, ECCC is making funding available to support action at the local level to restore water quality and aquatic ecosystem health by completing actions identified in AOC Remedial Action Plans (RAPs).

The purpose of the 2024-2025 Call for Proposals is to solicit project proposals that implement actions identified in the AOCs’ most current RAPs, and contribute to the restoration of beneficial uses and the completion of actions in AOCs. Proposals must clearly demonstrate how the project will contribute to these goals.  

Eligible recipients

Applicants may include:

  • Conservation Authorities
  • Indigenous organizations, governments, individuals, boards, commissions, communities, associations, and authorities
  • Municipalities
  • Not-for-profit organizations, such as charitable and volunteer organizations, professional associations, and non-governmental organizations Research, academic and educational institutions
  • Local organizations
  • For profit organizations

Provincial government agencies are not eligible for funding.

Types of projects eligible for funding

Remedial Action Plans have been developed for each Canadian Great Lakes AOC. These plans identify activities required to restore AOC water quality and aquatic ecosystem health. Eligible projects contribute directly to removing identified Beneficial Use Impairments (BUIs) through action, science or engagement. Examples of eligible projects include:


  • restoring degraded habitat
  • remediating contaminated sediment
  • point and non-point pollution control


  • conducting science and monitoring to inform remedial action planning and implementation
  • surveillance and monitoring processes to track the effectiveness of remedial measures and confirm restoration of beneficial uses


  • Community engagement for decision making
  • Community engagement for RAP implementation
  • Develop and maintain resources for RAP decision making


  • For applicants proposing Engagement projects, a detailed work plan will be negotiated based on the Project Work Plan (Section 5) details provided in application.
  • Any approved project will be required to report on performance indicators as part of final reporting. 
  • Refer to Appendix B for a list of RAP websites.
Funding details
  • funding is available on an annual basis
  • Great Lakes FEI may fund up to 100% of the project costs; however, project proponents are strongly encouraged to seek other sources of funding and/or in-kind project support
  • projects may be multi-year in nature, with a recommended maximum duration of three years
Eligible costs

Only costs directly attributed to carrying out the project will be eligible for funding, including:

  • human resource costs, including salaries and benefits
  • management and professional service costs, such as accounting, monitoring, communications, official languages translation, audit and legal charges
  • travel
  • material and supplies
  • printing, production and distribution costs
  • equipment and Capital Assets purchase or rental
  • vehicle rental and operation costs
  • contractors required to perform activities related to the project
  • cost associated with land acquisition, such as efforts to secure a conservation easement (but note that actual costs of land acquisition are not an eligible cost)
  • a reasonable share of overhead and/or administrative costs
  • any GST/HST that is not reimbursable by Canada Revenue Agency and any PST not reimbursable by the provinces
  • other incremental expenditures directly related to the project (as pre-approved by ECCC)

Costs, other than those herein allowed, are ineligible unless specifically approved in writing by the Minister of Environment and Climate Change or his/her representatives at the time of project approval. For all costs, only those deemed to be a reasonable share for completing the project shall be considered eligible. Note that Great Lakes FEI does not provide funding for capital or operating costs of municipal infrastructure or land acquisition.

Selection method

Project proposals will undergo a two-stage review process:

  1. administrative review by ECCC to ensure applications are complete and meet program eligibility requirements
  2. project evaluation by ECCC against evaluation criteria. ECCC may seek advice on proposal submissions from external advisors with knowledge and expertise relevant to the proposal; however, approval decisions will be made by ECCC
Administrative review

To be considered eligible for funding, project proposals must meet the following requirements:

  • the proposed project addresses priorities of the Remedial Action Plan or workplan of an AOC
  • the project applicant is eligible to receive funding
  • the geographic scope is limited to Canadian AOCs
  • funding will not be used for capital or operating costs of municipal infrastructure or land acquisition
Project evaluation

Eligible project proposals will be assessed on the extent to which proposals meet the following evaluation criteria:


  • the proposed project addresses issues in an AOC identified for completion of remedial action in the Canada–Ontario Agreement on Great Lakes Water Quality and Ecosystem Health and Remedial Action Plans
  • the proposed project will achieve a significant environmental result in the AOC
  • the proposed project will help redesignate a BUI(s) or identify priority remedial actions
  • the proposed project will help redesignate BUIs through coordinated information exchange, and public and stakeholder engagement
  • the importance of implementing the project in the current year(s) proposed is explained

Project feasibility / likelihood of success:

  • the proposed project is technically feasible
  • the project timeline and work plan are realistic
  • the project proponent has, or has access to, the necessary technical expertise and staff to effectively implement the project
  • the necessary permits have been identified and/or received
  • the project proponent has experience planning and managing this type of project

Additional benefits:

  • the proposed project provides benefits to other Great Lakes FEI priorities
  • the proposed project aligns well with other priority remedial actions in the AOC
  • the proposed project includes public outreach and/or engagement with the public, Indigenous communities and key stakeholders, which would benefit the Remedial Action Plan and AOC Program
  • the proposed project includes innovative approaches that could accelerate achievement of BUI delisting criteria or the delisting of the AOC

Value for money:

  • the proposed project represents good value for dollars invested
  • the proposed project includes cash and/or in-kind contributions from other sources
Description of the online application process and application sections

Environment and Climate Change Canada requires that applications to the Great Lakes FEI be submitted online via the Grants and Contributions Enterprise Management System (GCEMS). The GCEMS is accessed through the department’s Single Window system.  For additional information on accessing the GCEMS through ECCC’s Single Window system, please see Appendix A.

The online Application Form for the Great Lakes FEI: Restoring AOCs funding stream includes nine sections:

  • Section 1: Tombstone Data
  • Section 2: Project Summary
  • Section 3: Great Lakes FEI – restoring Areas of Concern (program-specific section)
  • Section 4: Project Budget
  • Section 5: Project Work Plan
  • Section 6: Evaluation Plan and Performance Measures
  • Section 7: Other Supporting Information
  • Section 8: Official Languages
  • Section 9: Certification

In Section 1: Tombstone Data, provide basic information about your group as well as contact information for the individual leading the application.

In Section 2: Project Summary, provide basic information about the proposed project, including the name and location of the project, the project start and end date, the project goals/objectives, a brief general description of the proposed project, the experience of project team members and the financial and management capacity of the organization submitting the project proposal. If your project is approved for funding, the summary description you provide in your application may be made available to the public.

In Section 3: Great Lakes FEI - AOCs (program-specific section), provide information about the proposed project, including the priority focus *(Action; Science; or Engagement); how the proposed project will assist with the restoration of beneficial uses within the AOC and the achievement of delisting targets; how the proposed project will assist with the completion of RAP recommended actions; a site description; and, details related to performance monitoring and the project budget.

*Projects must address one or more of the following priority focuses:


Implement remedial actions that restore beneficial uses in AOCs, including habitat rehabilitation, point and non-point source pollution control, contaminated sediment remediation, urban storm water/combined sewer overflow control.


Conduct science and monitoring to assess the status of beneficial use impairments against delisting criteria and inform remedial action planning and implementation.


Support essential elements of engagement in Remedial Action Plan decision making to restore beneficial uses. Engagement will inform decisions related to projects, work plans, criteria, monitoring and assessment. Engagement may include virtual / social media presence for information on which RAP decisions are based.

In Section 4: Project Budget, provide the total amount of ECCC funding that is being requested for the proposed project, outline the project’s budget and give an estimation of its forecasted expenses organized according to a set of pre-defined cost categories (such as salaries and wages; management and professional services; travel; and, material and supplies costs). The estimated cost of all project expenditures should reflect fair market values at the standard rate for that product or service in your area.

In this section, you are also required to provide details regarding the project's fiscal year breakdown. Determine the number of years of support from ECCC that your project requires and indicate how the total amount of support requested will be allocated on an annual basis.

Disbursement of funds - Identify if your project involves the further disbursement of funds (such as landowner stewardship programs). 

Finally, in this section you are required to indicate other funding sources for the project if applicable. Provide letters of financial/in-kind support for the project in the Other Supporting Information section.

In Section 5: Project Work Plan, provide details on the activities that will be undertaken for the duration of the project.

In Section 6: Evaluation Plan and Performance Measures, provide details on how the expected results and successes of the project will be measured. Describe monitoring, or other follow-up activities, designed to assess the project’s performance.

For Science and Engagement projects, measures should be described in the context of delisting criteria/targets/workplans for the AOC.

For Action projects, specific performance measures should be used. Choose at least three indicators from either group that apply to your project.

  • Point and non-point source pollution control performance indicators
    • Cover Crop: Number of projects, Total size of project sites (ha)
    • Conservation Tillage: Number of projects, Size of project sites (ha)
    • Livestock Fencing: Number of projects, Total metres of fencing (m), Amount of N diverted (kg), Amount of P diverted (kg)
    • Manure Storage-Wash Water: Number of manure storage projects, Amount of manure contained (m3), Number of wash water projects, Amount of wash water contained
    • Septic Tank Upgrades: Number of septic system upgrades
    • Reductions in pollutant loadings (phosphorus, suspended solids, oil and grease, and other relevant pollutants)
    • Reduction in combined sewer overflows
    • Number of low impact development (LID) projects completed
    • Volume of water detained or diverted from watercourses by LID projects


  • Habitat rehabilitation projects performance indicators
    • Wetland Habitat: Area rehabilitated (ha)
    • Prairie/Meadow Habitat: Area rehabilitated (ha)
    • Forest Habitat: Area rehabilitated (ha)
    • Riparian Habitat: Length rehabilitated (km)
    • Aquatic Habitat: Area rehabilitated (ha), Number of aquatic plants planted
    • Barriers to Fish Migration: Number of barriers removed, Potential fish habitat unlocked (km)
    • Buffer Strips: Number of buffer strip projects, Buffer Strip Area (m2)
    • Herbaceous Plants: Number of herbaceous plants planted
    • Tree and Shrub Planting: Number of planting projects, Number of trees and shrubs planted
    • Wildlife Habitat: Number of wildlife habitat installation projects, Installation Type & Quantity (Platform, Nesting Box, Hibernacula, Others)
    • Soft Shoreline: Length of soft shoreline engineering (km)
    • Soil Erosion: Area of grassed waterways (m2), Number of rock chutes and outlet stabilization structures,
    • Number of streambank stabilization projects through bioengineering, Length of streambank stabilization projects through bioengineering (m)

For assistance with developing appropriate performance measures please contact Areas of Concern program staff at of

In Section 7: Other Supporting Information, provide further information relevant to the project that was not captured elsewhere in the application if needed. This may include water and sediment quality data, scientific publications, permit applications, material estimates, project schedule, and letters of financial/in-kind support for the project.

In Section 8: Official Languages, provide information related to the need to accommodate official language minority communities with respect to the proposed project’s activities.

In Section 9: Certification, certify that information provided in the Application Form is accurate and that you, as the applicant, have authorization to sign on behalf of the group.

Other instructions

Applicants are encouraged to provide the details necessary to give a full response to each section of the Application Form but should be as concise as possible.

Please ensure that all sections of the Application Form are complete prior to submission. Incomplete applications will not be reviewed.

Applicants may include additional information or documents with their application (such as examples of possible products, photographs, maps, etc.). If submitting additional material, it must be clearly marked and referenced accordingly in the relevant section of the application. All such material must be submitted in accordance with the instructions found online in the Other Supporting Information section.

Applicants are encouraged to identify any additional partner funding and/or in-kind project support that has been obtained and/or that is being sought. Please note that while this is not a requirement, applications demonstrating other sources of financial and/or in-kind support will be scored favourably when evaluated on value for money.

Note: if you are unable to complete and submit your application via the online application portal and wish to discuss options, please contact

Deadline and submission instructions

Applications are due by 11:59 p.m. EST on February 16, 2024. Late submissions will not be considered.

Once departmental approvals in principle have been confirmed, all applicants (both successful and unsuccessful) will be notified in writing. If your project is approved in principle, you will be contacted to negotiate a Contribution Agreement, which outlines the terms and conditions of funding. Please note that the letter of notification informing that your project has been approved in principle will also be shared with relevant federal MPs. We will work towards completing this process within 40 working days. Please note that meeting this standard for the development of a Contribution Agreement is a shared responsibility and largely depends on you submitting all required documentation to ECCC officials in a diligent and timely fashion.  

Project implementation can begin after formal notification of project approval, pending the execution of project agreements or contracts where applicable.

If a Contribution Agreement is signed, expenditures made by your organization towards the project after the date of official notification and before the Contribution Agreement is signed may be considered for reimbursement.

For clarification on any of the above, please do not hesitate to contact

Appendix A – the online application process

Environment and Climate Change Canada requires that applications to the Great Lakes FEI: Restoring AOCs funding stream be submitted online via the Grants and Contributions Enterprise Management System (GCEMS). The GCEMS is accessed through the department’s Single Window system.

To sign in to the department’s Single Window system select your language preference on the welcome page and when prompted to choose a sign-in method, select the GCKey sign-in option. If you already have a GCKey username and password enter them in the appropriate spaces.

If you do not have a GCKey username and password proceed through the sign-up process to obtain your username and password.

New users to the Single Window system will then be prompted to enter their email address and guided through a process to create a user profile.

In order to gain access to the link that will allow you to navigate to the GCEMS, you must add an organization to your profile. On the menu select “Organizations” and follow the instructions on the web page that opens. Note that when entering the organization’s business number you may use one of the following; business number; GST number; charitable number/non-profit organization registration number; or First Nations Band number. Once you have added your organization, select “Home” on the menu to navigate to the webpage that contains the link to the GCEMS.

Once you have accessed the GCEMS site, click on the link “View funding opportunities” on the left hand side of the GCEMS “My applications” webpage. On the “View funding opportunities” webpage, locate the Great Lakes FEI in the “List of opportunities” table and view the funding opportunity information by clicking on the associated link in the “Action(s)” column. On the “View funding opportunity information” webpage, click on “Apply” to open the online application process for the Great Lakes FEI: Restoring AOCs funding stream.

Information on how to access and use ECCC’s Single Window system.

For technical assistance with ECCC’s Single Window system, please contact

Information on how to access the GCEMS.

For technical assistance with the GCEMS, please contact

Appendix B – Remedial Action Plan websites

Project proposals are not being solicited for the following AOCs: Nipigon Bay, Jackfish Bay, Peninsula Harbour, Spanish Harbour, and Port Hope Harbour.

Proponents are encouraged to contact local RAP coordinators or ECCC AOC staff at to discuss project proposals.   

AOC Web site
Thunder Bay, Nipigon Bay, Jackfish Bay, Peninsula Harbour INFOSuperior
St. Marys River Binational Public Advisory Council for St. Marys River Area of Concern
Detroit River Detroit River Canadian Cleanup
St. Clair River Friends of St. Clair
Niagara River Niagara River Remedial Action Plan
Hamilton Harbour Bay Area Restoration Council
Toronto and Region
Toronto and Region Remedial Action Plan
Bay of Quinte Bay of Quinte Remedial Action Plan
St. Lawrence River
St. Lawrence River Remedial Action Plan

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