| Frequent San Juan Island Destinations | —— | Other Frequent Destinations |
| - Friday Harbor | - Seattle (Boeing field and Sea-Tac) | |
| - Orcas Island (Eastsound) | - Tacoma (Narrows Airport) | |
| - Lopez Island | - Port Angeles | |
| - Roche Harbor | - Port Townsend | |
| - Shaw Island | - Olympia | |
| - Stuart Island | ||
| - Waldron Island | Frequent Canadian Destinations | |
| - Crane Island | - Victoria, B.C. | |
| - Decatur Island | - Vancouver, B.C | |
| - Sinclair Island | - Nanaimo, B.C. | |
| - Center Island | - Cambell River, B.C. | |
| - Blakely Island | - Tofino, B.C. | |
| - Point Roberts (U.S) | - Port Hardy, B.C. |
