Small stream:
* Brook
* Rivulet
* Run
* Streamlet
Narrow inlet of the sea:
* Inlet
* Cove
* Bayou (specifically for inlets in the southeastern US)
Informal, general term:
* Stream
* Watercourse
* Gulch (more rugged, often with steep sides)
The best synonym will depend on the specific situation and what you want to emphasize.