The U. S thus began dealing with the pirates since 1784 to 1816 after the successful second Barbary war. Since the beginning, Jefferson was for peace but he always weighed upon paying tribute to Barbary States or waging war on them to end the problem once and for all (Parton 405-424). He held the belief that paying tributes would only lead to pirates carrying out more attacks and asking for more ransom. As such, he favored war than tribute but the nation had just been out of the revolutionary war hence had a constrained budget and a weak army hence not ready for any war.
At the circumstance, paying tribute was the only option. At first, America had no serious problems since their fleet went in convoy with British fleet and Algiers was in war with Portugal hence Portugal protected American ships. The first ship was seized by Moroccan pirates in October 1784 but freedom of the crew was negotiated by the Spanish government. Jefferson as the U. S minister of France sent envoys to Morocco and Algeria to negotiate equal treaties and secure the freedom of captured crew in Algeria and in June 1786, a treaty was reached with Morocco.
The treaty sought to set free any captured Americans by Morocco or any other Barbary state as long as it was docked on a Moroccan port. However, the other Barbary States were not willing to make peace or sign treaties yet. In 1785, Algiers pirates captured the crew of Maria and Dauphin and kept them in captivity for more than a decade pending payment of tribute and ransoms and were joined by other crews from more captured ships (Parker 48-58; Roberts & Roberts 163-170).
At the time, the U. S was undergoing economic problems hence was unable to raise a navy or tribute to protect its ships and a coalition of weaker naval powers by Jefferson to defeat Algiers was unsuccessful. Though, American ships were protected by Portugal in Gibraltar, in 1793 Portugal and Algeria reached a truce hence increasing vulnerability of American ships. In 1795, a tribute of $ 1 million was agreed upon with Dey Muhammad of Algeria leading to release of captives and U. S continued to do so for the next fifteen years.
This was to ensure safe passage of merchant ships and also the release of hostages but it was very costly for the U. S which was operating on a constrained budget. Thomas Jefferson was thus always against this payment of tributes. The U. S was a peaceful nation hence sent diplomats Joel Barlow, Joseph Donaldson and Richard O’Brien to negotiate treaties with the rest of Barbary states (Algiers, Tunis & Tripoli) in 1795 (Office of the Historian).
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Parker, Richard B. Uncle Sam in Barbary. Gainesville, Fla: University Press of Florida, 2004.
Parton, James. Jefferson, American Minister in France. Atlantic Monthly. 30.180 (1872): 405–424
Thomas Jefferson, First Annual Message to Congress, December 8, 1801, in PTJ, 36:58-59
Woods, Thomas. Presidential War Powers. 7 July, 2005. LewRockwell.com. Web. 21 April, 2014.