The Muskoka Watershed Council area of interest encompasses the Muskoka River Watershed as well as portions of the Black River and Severn River Watersheds. Collectively, this area consists of twenty subwatersheds.

The 2010 Muskoka Watershed Report Card includes reports for each of these subwatersheds.

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• Big East River Subwatershed
• Cardwell Lake Subwatershed
• Gibson Lake Subwatershed
• Huntsville Lakes Subwatershed
• Kahshe Lake Subwatershed
• Kawagama Lake Subwatershed
• Lake Muskoka Subwatershed
• Lake of Bays Subwatershed
• Lake Waseosa Subwatershed
• Lakes Rosseau and Joseph Subwatershed
• Lower Black River Subwatershed
• Moon River Subwatershed
• North Branch Muskoka River Subwatershed
• North Simcoe Subwatershed
• Oxtongue River Subwatershed
• Severn River Subwatershed
• Skeleton Lake Subwatershed
• South Branch Muskoka River Subwatershed
• Three Mile Lake Subwatershed
• Upper Black River Subwatershed