Muskoka Watershed Council undertakes a number of programs, many in conjunction with other organizations. These programs include:
- Integrated Watershed Management
- Doug Cross Stewardship Recognition Program
- The Natural Edge Shoreline Re-naturalization Program
- Love Your Lake Shoreline Assessment and Stewardship Program
- Algae Monitoring Program
- Clean & Green 13
- Best Practices Program
- Outreach & Education
- Watershed Inventory Project