| São Tomé River | |
| Pushpin Map: | Brazil |
| River System: | Juruena River |
| Source1 Location: | Mato Grosso state |
| Mouth Coordinates: | -8.1371°N -58.2849°W |
| Subdivision Type1: | Country |
| Subdivision Name1: | Brazil |
The São Tomé River is a river of Mato Grosso state in western Brazil. It is a tributary of the Juruena River.
All of the river's sources are in the Juruena National Park, one of the largest conservation units in Brazil.The São Tomé basin occupies 23% of the park.