Wolastoq/Saint John River Freshwater Ecosystem Initiative – Applicant guide 2027-2028

About the Applicant Guide

The Applicant Guide is designed to assist eligible organizations in applying to the Wolastoq/Saint John River Freshwater Ecosystem Initiative. You are welcome to contact the Canada Water Agency (CWA) if you require clarification on the information contained in this guide. If you require assistance with the Grants and Contributions Enterprise Management System (GCEMS), please contact GCEMS directly. 

The Wolastoq/Saint John River Freshwater Ecosystem Initiative

The Wolastoq/Saint John River is binational and inter-jurisdictional waterway with significant ecological, economic, and recreational value. A Canadian Heritage River, the Wolastoq/Saint John River is the largest river in the Maritime provinces. It flows for more than 600 km through Maine, Quebec (QC), and New Brunswick (NB), before emptying into the Bay of Fundy. A 115 km stretch of the river represents the international boundary between Canada and the United States. The watershed is part of the traditional territory of the Wolastoqey people, who maintain an inherent connection to the Wolastoq (meaning “the beautiful and bountiful river”).

The ecological health of the watershed is, however, threatened by numerous cumulative factors. Various land uses (i.e., agricultural, industrial, and urban development), combined with the effects of climate change, are impacting freshwater quality. Major concerns include high levels of nutrients and bacteria, which contribute to harmful algal blooms (cyanobacteria) and the proliferation of benthic mats. In addition, the increasing presence of harmful pollutants and emerging contaminants is contributing to the stress and decline of freshwater ecosystems.

Figure 1: Wolastoq/Saint John River Sub-Basins

As part of the Federal Freshwater Action Plan, the Government of Canada is implementing the Freshwater Ecosystem Initiatives (FEI) to restore and protect freshwater ecosystems of national significance. FEI investments support actions that address regional freshwater challenges and priorities. The Wolastoq/Saint John River FEI will provide financial support for eligible projects that will improve the water quality and maintain ecological health of the Wolastoq/Saint John River Watershed.  

1. Program Priorities and Eligible Projects

The Wolastoq/Saint John River Freshwater Ecosystem Initiative will fund projects to be implemented by domestic partners in the Canadian portion (Quebec/New Brunswick, see Figure 1 for a map of watershed boundaries) of the Wolastoq/Saint John River watershed that address at least one of the following three program priorities:

1. Nutrient Reduction: Projects will implement actions to reduce nutrient loading and increase public awareness and engagement on water quality protection.

Types of projects eligible for funding include:

• Development and testing of innovative tools, technologies, techniques, and demonstration projects that reduce nutrient loading into the river.
• Implementation of beneficial management practices (BMPs) known to reduce nutrient loading through prevention, reduction, and mitigation of nutrient loading to waterbodies.
• Training, outreach and/or education to support the implementation of nutrient reduction actions.

2. Advancing Science and Knowledge: Projects will increase knowledge and scientific understanding in one of the following two areas of focus:

• Impacts of Excess Nutrients and Harmful Algal Blooms/Benthic Mats: Projects will increase knowledge to better understand the state of, threats, and pathways of excess nutrients, cyanobacteria, algal blooms/benthic mats, and their impacts on water quality and ecosystem health. Projects will involve the collection, analysis and sharing of information to support informed decisions and actions to address these freshwater issues.

OR

• Harmful Pollutants: Projects will increase knowledge to better understand the state of, threats, and pathways of harmful pollutants and contaminants of emerging concern and their impacts on water quality. Projects will involve the collection, analysis, and sharing of information to support informed decisions and actions to address these freshwater issues.

Types of projects eligible for funding include:

• Assessment of stressors, risks and baseline environmental conditions related to nutrients and harmful algal blooms/mats.
• Measurement, monitoring, modelling, or analysis of nutrients and harmful pollutants on:
  • The impacts on ecosystem health.
  • Ecosystem changes or trends.
  • Multiple stressors and related cumulative effects.
• Community-based monitoring to supplement existing water quality monitoring data.
• Development of scientific tools, systems, and innovative technologies.
• Identification of data and research gaps, sharing of knowledge and information, and/or development of data management strategies.
• Advancing the understanding of the impacts of climate change on nutrient pathways and loading, and other harmful pollutants

3. Indigenous Knowledge, Capacity Building, and Engagement: Projects will support Indigenous-led efforts to increase knowledge of freshwater issues, and/or build capacity of Indigenous organizations and communities to address freshwater issues.

Types of projects eligible for funding include:

• Gathering of Indigenous Knowledge and applying Indigenous Knowledge systems to inform actions and decision making related to freshwater issues.
• Building capacity, outreach, training, and engagement for Indigenous organizations and communities to research and address freshwater issues.
• Data collection, monitoring and trend analysis related to water quality and impacts of water quality on ecosystem health.
• Opportunities for Indigenous and non-Indigenous organizations to build relationships and work collaboratively on identifying common priorities and partnerships to address freshwater issues.
• Projects that bring together diverse knowledge systems and perspectives to support actions and decision making related to freshwater issues.

2. Projects Not Eligible for Funding

The following types of projects are not eligible for funding under the Wolastoq/Saint John River Freshwater Ecosystem Initiative:

• Monitoring and data collection as stand-alone projects. These projects must be part of an overall trend analysis, or integrated planning process.
• Projects that have a single issue ‘action’ focus such as stream clean-ups, attending conferences, training, workshops and meetings.
• Ocean-based and fish-based ecosystem projects are not eligible.
• Infrastructure projects are not eligible.

3. Eligible Applicants

Canadian-based organizations are eligible to apply and include:

• Not-for-profit organizations such as charitable and volunteer organizations, professional associations, and non-governmental organizations and groups.
• Indigenous organizations, governments, boards, communities, and associations.
• Research, academic, and educational institutions.
• Municipal and local governments.

Although business / industry, federal, and provincial governments are not eligible funding recipients, they are encouraged to provide support and/or funding to eligible partners on proposed projects.

4. Eligible Project Costs

The following project costs are eligible:

• Human resource costs, including salaries and benefits.
• Management and professional service costs such as accounting, monitoring, communications, official language translation, audit, and legal fees.
• Hospitality, travel and venues/conference expenses that are attributed directly to carrying out the project (in accordance with the Treasury Board Secretariat’s Directives on Travel, Hospitality, Conference and Event Expenditures.
  • Hospitality expenditures can include costs related to Indigenous ceremonial offerings to be utilized or consumed during meetings or ceremonies such as traditional medicines, cultural foods, tea, and sacred plants.
• Costs associated with an Indigenous participation or ceremony.
• Monetary Honoraria offered to Indigenous Elders and/or Knowledge Keepers related to specific participation activities which may include but not are not limited to translation and interpretative costs, leading a traditional opening/closing ceremony and/or prayer, the sharing of Traditional Knowledge and protocols, (including spiritual advice to individuals), and demonstrating traditional art and other practices.
• Materials and supplies.
• Printing, production, and distribution costs.
• Equipment and capital asset purchases or rental.
• Vehicle rental and operation costs.
• Contractor services required to perform activities related to the project.
• Costs associated with land securement (e.g. leases, easements, covenants or servitudes).
• A reasonable share (20% or less) of overhead and/or administrative costs directly attributed to project delivery.

Buy Canadian Policy

The Government of Canada is making Canada its own best customer by strengthening domestic industries, supporting domestic workers, and building a more resilient and diversified economy in a rapidly changing global trade environment. This approach also supports Indigenous business growth, innovation, employment and supply chains across Canada.

As the Government of Canada is committed to advancing this federal priority, you are encouraged to prioritize Canadian goods and services, including Indigenous goods and services, in your proposed project.

5. Funding Details

Projects are eligible for funding up to a maximum of $200,000 per project. Projects can be single or multi-year in nature but must be completed by March 31, 2030.

Wolastoq/Saint John River Freshwater Ecosystem Initiative funding must be requested for each year of the project to be eligible.

The current Call for Applications is for projects that will begin during the 2027/2028 fiscal year, with project start dates of April 1, 2027, or later. Projects that are not funded can be re-submitted through a future call for applications.

6. Financial Matching Requirements and Calculation Guidelines

A minimum of 30% of the total project funding must be obtained from sources other than the Government of Canada. For example, a proposal for a $100,000 project could include up to $70,000 in Government of Canada funding and a minimum of $30,000 from non-federal sources. Employment support programs within Employment and Social Development Canada and programs for Indigenous peoples within Indigenous Services Canada are exempt from this requirement. Other sources of funding may be in the form of cash or in-kind contributions, or a combination of both.

In-kind support may include donations of:

• Equipment, materials, and/or office space.
• Volunteer time for project activities, coordination, or professional services.
• Expertise from consultants, Elders, or academics.
• Any other donated goods or services that contribute to covering the costs of the project.

The maximum level (stacking limit) of total Canadian Government assistance (federal,

provincial, territorial and municipal assistance for the same eligible expenditures) for projects will not exceed 100% of the total eligible expenditures of a project. Applicants should declare prospective sources of funding for the project including federal, provincial, territorial, municipal and other sources of funding in their application.

Table 1 provides an example of the calculation.

Table 1: Example of a Matching Contribution Calculation

7. Permits and Federal Lands

Applicants are responsible for conducting the necessary research to determine whether laws or mandates apply to any of the activities listed in the application. It is recommended that applicants verify relevant federal, provincial/territorial, and municipal legislation and regulations relating to the project’s activities and/or location(s).

Permits

If permits or authorizations are required for the project, these must be identified in the application. If not yet obtained, ensure the timeline for obtaining these approvals is included in the project’s work plan.

Federal Lands

Applicants must review their project locations and activities and determine if any activities will occur on federal lands. Projects occurring on federal lands may be required to complete an Impact Assessment.

According to the Impact Assessment Act, federal lands are defined as:

a) Lands that belong to His Majesty in right of Canada, or that His Majesty in right of Canada has the power to dispose of, and all waters on and airspace above those lands, other than lands under the administration and control of the Commissioner of Yukon, the Northwest Territories or Nunavut;

b) the following lands and areas:

i. the internal waters of Canada, in any area of the sea not within a province;

ii. the territorial sea of Canada, in any area of the sea not within a province;

iii. the exclusive economic zone of Canada;

iv. the continental shelf of Canada; and,

c) reserves, surrendered lands and any other lands that are set apart for the use and benefit of a band and that are subject to the Indian Act, and all waters on and airspace above those reserves or lands (territoire domanial).

8. Performance Indicators

Applicants are required to report on one or more of the key performance indicators from the list below. It is recommended that groups report on all indicators that apply to the project, andproject and explain how the target numbers were calculated.

• Total number of sites where samples were collected (# of sites)
• Area of land restored/conserved (# of hectares)
• Number of beneficial management practices/plans developed / implemented leading to environmental improvements (# of practices, plans)
• Number of mitigation measures implemented and/or improved to reduce nutrients or harmful pollutant inputs (# of mitigation measures)
• Amount of phosphorus reduced/diverted (kg/year)
• Number of contributing partners or organizations (# of partners/organizations)
• Number of knowledge transfer and sharing events (# of presentations, meetings)
• Number of people engaged in outreach/communications/training (# of people engaged)
• Number of reports/papers compiled and published (not including required CWA reporting) (# of reports/papers)
• Number of native trees and/or shrubs planted in the project-supported restoration areas (# of trees planted during the project, # of shrubs planted during the project).
• Survival rate of native trees and/or shrubs planted in project-supported restoration areas (% = 100 x [trees and/or shrubs alive at the end of the project ÷ trees and/or shrubs planted at the start of project]).

9. Funding Application Submission Process

Applicants must submit their project proposal using the Grants and Contributions Enterprise Management System (GCEMS), Canada Water Agency’s (CWA) online application system.

Note: The online application system (GCEMS) is shared between CWA and ECCC.  References to ECCC in the system apply to both organizations. 

It is strongly recommended that applicants complete the budget in GCEMS at least 24 hours prior to the deadline to allow sufficient time to resolve any errors. The applications that are not submitted by the deadline will not be considered.

GCEMS Applicant User Guide: The GCEMS Applicant User Guide contains step-by-step instructions on how to apply for funding, including information on how to create, edit and submit project proposals.  You can access it by clicking the following link: Grants and Contributions Enterprise Management System

For technical assistance when using GCEMS, please contact the GCEMS team directly at: sgesc-gcems@ec.gc.ca.

10. Funding Application Selection Process

The Wolastoq/Saint John River Freshwater Ecosystem Initiative project funding decisions are made through a competitive, merit-based process. Eligible projects will be evaluated on the quality and completeness of the application.

Submitted applications will undergo a three-stage review process:

1. Administrative review by program staff to confirm eligibility (projects considered not eligible will be notified at the end of this stage).
2. Technical review by subject-matter experts to evaluate scientific and technical feasibility, including methodology.
3. In-depth review of the funding application to determine the extent to which it aligns with the program's priorities and criteria for project selection.

11. Evaluation Criteria

Eligible applications will be assessed against, but not limited to, the following criteria:

• Demonstrates strong alignment with the Wolastoq/Saint John River Freshwater Ecosystem Initiative program’s priorities. The application must clearly demonstrate the need for the project, its importance to the health of the Wolastoq/Saint John River, and its contribution to the expected outcomes of at least one of the program's three priorities.
• Builds partnerships through collaboration with other organizations. The application must demonstrate that the proposed project is supported by appropriate and complementary partnerships that bring together, as warranted by the nature and objectives of the project, non-governmental organizations, governments, academic institutions, Indigenous communities, and private-sector or industry partners. The application must clearly identify the roles, responsibilities, and contributions of each partner or collaborator, as well as the value added through these collaborative arrangements, including capacity, expertise, resources, and stakeholder engagement. The application should further demonstrate that the participation of key partners, funding contributors, and stakeholders required to achieve the proposed outcomes has been secured, and that the proposed partnerships are substantive, effective, and appropriately aligned with the project's objectives and intended results. Development of partnerships through collaboration with other organizations.
• Is scientifically and/or technically sound. (For projects that include scientific, research, and/or nutrient reduction components.) The application must provide detailed information on methodology and techniques used in order to evaluate the scientific/technical merit of the project. The application must demonstrate the project will be based on sound scientific principles and that techniques used are scientifically valid, accepted, appropriate and applicable.
• Indigenous-led efforts and/or Indigenous Knowledge. Projects including these elements should describe how Indigenous organizations or communities are actively engaged in the design AND delivery of the project. The application must also describe how the project contributes to strengthening knowledge and understanding of freshwater issues, as well as enhancing the capacity of Indigenous organizations and communities to take action to protect and improve the health of freshwater ecosystems.
• Builds on/integrates existing research and Knowledge/Indigenous Knowledge. Project activities are expected to build on existing research and knowledge wherever possible. The Canada Water Agency recognizes the value of both traditional and scientific knowledge and encourages their integration their integration into the design and implementation of projects. Applications should demonstrate that the proposed project is informed by relevant and credible sources of information and supports activities that are likely to achieve tangible and sustainable environmental outcomes.
• Communication of results and knowledge. Organizations are encouraged to seek opportunities for knowledge transfer to other organizations that would extend the reach of project outcomes. A competitive application will demonstrate a commitment to disseminate results and findings to ensure that benefits are shared with a wide array of stakeholders and achieve broad impacts throughout the watershed.

12. Notification and Reporting Requirements

All applicants will be notified by email of the decision regarding their application, regardless of whether it is selected for funding. If your project proposal is selected and funding is approved, you will be contacted to negotiate a Contribution Agreement, which outlines the terms and conditions of funding. Federal MPs and/or their team may be advised about the approval of a project and may be provided with information in the project application including applicant’s name, project title, project description, project location, funding amounts and contact information.

Funding is conditional on the successful negotiation of a Contribution Agreement between the applicants and the CWA. Each Contribution Agreement must include written confirmation of all funding sources, a summary of project design, delivery, progress evaluations and anticipated results, as well as a budget forecast. All of these components must be accurately completed before the agreement can be signed.

All approved recipients are required to submit reports to CWA throughout the duration of the project as outlined in the Contribution Agreement. Payments are based on reporting and cannot be made until a report has been submitted, reviewed, and approved by a CWA project officer.

Once a project has been completed, a final report is required. The final payment (the minimum 10% holdback) will not be released until a final report has been submitted and approved by CWA.

If you have any questions, please do not hesitate to contact us at the following email address: wolastoqsaintjohn-wolastoqsaintjean@cwa-aec.gc.ca.

Contact information

Related links

• Grants and Contributions Enterprise Management System Applicant User Guide
• Projects funded under the Wolastoq/Saint John River Freshwater Ecosystem Initiative