The Skagit River System Cooperative works in partnership with a number of agencies, including:
- Sauk-Suiattle Indian Tribe
- Swinomish Indian Tribal Community
- Northwest Indian Fisheries Commission
- Washington Department of Natural Resources
- United States Forest Service, Mt. Baker-Snoqualmie National Forest
- Skagit County
- The Nature Conservancy
- Seattle City Light
- Skagit Watershed Council
- Skagit Fisheries Enhancement Group
- Skagit Land Trust
- Washington Department of Fish and Wildlife