What did Jefferson do to stop the Barbary States from pirating American ships?

He created the Embargo Act and he also launched the US navy at the Barbary States.

Explanation:

Since the Barbary Pirates were stealing US merchant boats, he first created the Embargo Act, which prohibited trade with other countries (at least for the time being). He then launched ships into the Mediterranean, resulting in the first Barbary War, that the US won.