- Schmidt Landing
- Scout Island
- Sego Island (historical)
- Sevenmile Corner
- Shadehill
- Shady Beach
- Shamrock Colony
- Shannon Colony
- Sharps Corner
- Sheffield
- Shelby
- Sheldon Trailor Town
- Shindler
- Silver City
- Silver Lake Colony
- Silver Valley Addition
- Sioux Falls Junction
- Sioux Village
- Sitka
- Skeleton Island
- Skunk Island
- Skunk Island (historical)
- Skyline Heights
- Slim Butte
- Smiths Park
- Smithwick
- Snake Creek
- Soldier Creek
- Sorum
- Sorum Addition