- San Juan
- San Juan Island
- Scott Island
- Seal Rocks
- Shaw Island
- Shirleyville
- Sixty-foot Rock
- Slate Island
- Snug Harbor
- Squab Island
- Seal Cove Rocks
- Ship Island
- Shoreline Drive
- Sister Islands
- Sitklan Island
- Slate Islands
- Slim Island
- Smeaton Island
- Snail Rock
- Snip Islands
- Snipe Island
- Square Island
- Stack Island
- Stag Island
- Sally Island
- Sea Otter Island
- Seal Islands
- Seal Rocks
- Sealion Rocks
- Semidi Islands