In 1808, Congress again approved funds to fortify the coastline, prompted by the prospect of another war with England. England was at war with France, which was ruled by Napoleon Bonaparte at the time, and although the United States had not taken sides in that conflict, in June 1807 the British attacked the U.S. ship Chesapeake, violating America's neutral status. The Chesapeake incident created serious tensions between the United States and Britain. Although the United States did not go to war for another four years, Congress saw a need for military readiness in this atmosphere of crisis.
Fort Trumbull was rebuilt under the new federal fortification program, which became known as the Second System. The new fort had five sides of uneven length made of masonry (stone or brick) and sod, and it was equipped with eighteen heavy guns. Frances Caulkins, New London's nineteenth-century historian, wrote that from "a military point of view" the new fort "was far superior to the former structure."
Congress declared war on Britain in June of 1812, although all the congressmen from Connecticut voted against it. By 1813, federal troops were stationed at Fort Trumbull, and British ships had imposed a tight blockade on New London Harbor. The British fleet remained positioned outside the harbor for most of the war, but never attacked New London. The British did attack Essex, a town on the Connecticut River, and Stonington, a coastal town near the Rhode Island border, in 1814.