The IJC has established various boards and task forces, consisting of experts from Canada and the United States, to help it carry out its responsibilities. Boards followed by IWI in the list below are actively participating in the International Watersheds Initiative.
- Council of Great Lakes Research Managers
- Great Lakes Science Advisory Board
- Great Lakes Water Quality Board
- International Air Quality Advisory Board
- International Columbia River Board of Control
- International Kootenay Lake Board of Control
- International Lake of the Woods Control Board
- International Lake Superior Board of Control
- International Niagara Board of Control
- International Osoyoos Lake Board of Control
- International Rainy Lake Board of Control IWI
- International Rainy River Water Pollution Board IWI
- International Red River Board IWI
- International Souris River Board IWI
- International St. Croix River Watershed Board IWI
- International St. Lawrence River Board of Control
Current task forces and study boards
- International Lake Champlain-Richelieu River Plan of Study Workgroup
- Health Professionals Advisory Board
- International Missisquoi Bay Study Board
- International Upper Great Lakes Study Board
- The International St. Mary and Milk Rivers Administrative Measures Task Force
Completed task forces and study boards
- Accredited Officers for the St. Mary-Milk Rivers
- International Lake of the Woods and Rainy River Watershed Task Force
- International St. Mary and Milk Rivers Administrative Measures Task Force
- International Lake Ontario – St. Lawrence River Study Board (Completed 2006)
- Upper Great Lakes Plan of Study Revision Team (Completed 2005)
- International Missisquoi Bay Task Force (Completed 2004)
- Indicators Implementation Task Force (Completed 2000)
- International Red River Basin Task Force (Completed 2000)
- Nuclear Task Force (Completed 1999)
- Lake Erie Task Force (Completed 1996)
- Indicators for Evaluation Task Force (Completed 1996)