However, by 1807 the Napoleonic Wars spilled into American waters. France and Great Britain's repeated offenses against American trade, threatened the United States' neutrality and sovereignty. Both countries prohibited neutral countries to trade with the other and Great Britain continuously stopped American ships in search for Royal Navy deserters. The Chesapeake Incident of 1807, possibly the best known occurrence of these offenses, brought Americans attention back to coastal defense. Five months after the Chesapeake Incident, Congress authorized three million dollars for the construction of a second system of American seacoast defenses.
This project was meant to improve and enlarge the first system, constructed at the end of the previous century. The second system would use stronger materials, such as brick and stone, and more appropriate designs for seacoast defense including star-shaped forts and those based on the military philosophies of French engineer Marc Rene', marquis de Montalembert. He, unlike Sebastien Le Prestre de Vauban another French military engineer, believed fortifications should resemble geometric shapes with levels of cannon. Finally, the system would be managed and controlled on a national level by the newly formed Army Corps of Engineers.
Charleston was one of the harbors along the Eastern seaboard tapped to receive newer seacoast fortifications as part of the second system. Remains of the first system were not only inadequate to properly defend the harbor, they were also mostly in ruin following several severe storms. Captain Alexander McComb oversaw the major projects: construction of a new Fort Moultrie on Sullivan's Island and Castle Pinckney on Shutes Folly Island.
Although the new forts in Charleston would not be used in battle till the Civil War roughly fifty years later, the threat Americans perceived in 1807 proved to be real. On June 18, 1812 the United States declared war on Great Britain beginning the War of 1812. Over the next three years, land and sea battles raged and in some cases seacoast defenses proved their worth. However, in other cases the system proved to be either inadequate or in newly acquired harbors absent all together. With the end of the War of 1812, the United States government addressed these issues authorizing the third system of American seacoast defenses to fill the gaps left by the previous systems.