There's a saying that a military prepares for the last war it fought. Such was the case with the United States. The experience at Tripoli taught America's naval and political leaders that gunboats could be effective in harbor defense. Navy Secretary Robert Smith, however, knew that gunboats alone would not be sufficient to meet America's defensive needs in the first decade of the 19th century. He asked the federal government in 1806 to provide for frigates, ships of the line, then gunboats for harbor defense.

Smith ran into a political buzzsaw: Treasury Secretary Albert Gallatin, a "fiscal superhawk" (to use a term from Six Frigates) who asked whether Smith's requested naval expense would cause more problems than it solved. While Smith had Congressional support, he was only able to wrangle funds for seaport fortifications and gunboats in April 1806. The same appropriations legislation limited the number of standing naval personnel; if gunboats were to be built, they would be operated by the equivalent of naval militia, by and large.

A year after Smith garnered $250,000 for gunboats, Jefferson asked Congress for $1 million more to build 200 additional gunboats. Congress complied with enough money to build 180.

There were multiple problems with the concept, to quote Six Frigates:

"As the first gunboats were launched and placed in service, criticism mounted. They were wet, cramped, and uncomfortable. It was often difficult to recruit full complements of seamen to man them. Officers took the first opportunity to be transferred into a frigate. Then a Norfolk gunboat capsized and sank in six fathoms of water, Stephen Decatur dryly asked a fellow officer: 'What would be the real national loss if all gunboats were sunk in a hundred fathoms of water?'"

The critics were, of course, right. Gunboats were ineffective in anything but a flat calm. They were incredibly fragile, usually sinking under a single shot from a larger vessel. They were difficult to man and operate ─ it was much more efficient to use the same number of crewmen on a frigate ─ and they were much more expensive than planned. Congress had expected each gunboat to cost about $5,000. The true cost was almost double that.

Congress authorized the construction of 278 gunboats between 1805 and 1807, but only 176 were built and still fewer were placed into service. The gunboat program was abandoned after Jefferson left office. It was a complete failure.