| Whatcom Creek Waterway | Whatcom, WA | 0 miles | SE |
| I and J Street Waterway | Whatcom, WA | 0 miles | NW |
| Inner Reach | Whatcom, WA | 0 miles | SW |
| Middle Reach | Whatcom, WA | 0 miles | SW |
| I and J Street Waterway | Whatcom, WA | 0 miles | NE |
| Squalicum Waterway | Whatcom, WA | 1.4 miles | NW |
| Portage Channel | Whatcom, WA | 6.6 miles | SW |
| The Portage | Whatcom, WA | 7.6 miles | SW |
| Hale Passage | Whatcom, WA | 8.1 miles | SW |
| Penguin Harbor | Skagit, WA | 13.2 miles | SW |
| Levant Passage | Skagit, WA | 14.3 miles | SW |
| Bellingham Channel | Skagit, WA | 14.5 miles | SW |
| Guemes Channel | Skagit, WA | 16.5 miles | SW |
| Rosario Strait | San Juan, WA | 17.7 miles | SW |
| Obstruction Pass | San Juan, WA | 17.9 miles | SW |
| Peavine Pass | San Juan, WA | 18.2 miles | SW |
| Burrows Pass | Skagit, WA | 19.9 miles | SW |
| Thatcher Pass | San Juan, WA | 20.9 miles | SW |
| Allan Pass | Skagit, WA | 21.3 miles | SW |
| Strait of Georgia | Whatcom, WA | 21.4 miles | NW |
| Harney Channel | San Juan, WA | 22 miles | SW |
| Upright Channel | San Juan, WA | 22.9 miles | SW |
| Swinomish Channel | Skagit, WA | 23.1 miles | SW |
| Lopez Pass | San Juan, WA | 23.7 miles | SW |
| President Channel | San Juan, WA | 23.8 miles | SW |
| Canoe Pass | Skagit, WA | 24.4 miles | SW |
| Deception Pass | Skagit, WA | 24.6 miles | SW |
| Northwest Pass | Island, WA | 24.6 miles | SW |
| Pole Pass | San Juan, WA | 24.9 miles | SW |
| Wasp Passage | San Juan, WA | 25 miles | SW |
| Careen Creek | San Juan, WA | 25 miles | SW |
| North Pass | San Juan, WA | 25.8 miles | SW |
| Spring Passage | San Juan, WA | 26.2 miles | SW |
| Boundary Pass | San Juan, WA | 26.6 miles | SW |
| Boat Channel | San Juan, WA | 26.6 miles | SW |
| San Juan Channel | San Juan, WA | 27.5 miles | SW |
| New Channel | San Juan, WA | 29.9 miles | SW |
| Spieden Channel | San Juan, WA | 30.2 miles | SW |
| Inner Passage | San Juan, WA | 30.7 miles | SW |
| Middle Channel | San Juan, WA | 30.8 miles | SW |
| Johns Pass | San Juan, WA | 31.1 miles | SW |
| Mosquito Pass | San Juan, WA | 32.9 miles | SW |
| Haro Strait | San Juan, WA | 34.5 miles | SW |
| West Pass | Snohomish, WA | 34.9 miles | SE |
| South Pass | Snohomish, WA | 35.9 miles | SE |
| Hat Slough | Snohomish, WA | 37.8 miles | SE |
| Saratoga Passage | Island, WA | 39 miles | SW |
| East Waterway | Snohomish, WA | 54.1 miles | SE |
| East Waterway | Snohomish, WA | 54.2 miles | SE |
| Admiralty Inlet | Jefferson, WA | 55.3 miles | SW |
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