During the Civil War, the port community of Bayport was an active area for blockade running. In April 1863, an expedition of Union sailors in seven launches and cutters entered the harbor where six blockade runners were in port.

Four of these vessels fled into the bayou where they grounded on the banks while a fifth vessel, the Helen, was burned by the raiding force. As the Union boats armed with howitzers headed for the sixth vessel, a schooner loaded with cotton, they exchanged fire with the Confederate battery of two cannons at Bayport and Confederate riflemen along the shore.

Before they reached the Confederate vessel, it burst into flames, presumably to prevent its capture, and the Union force withdrew. The Union force suffered one wounded while the Confederate losses were one killed and three wounded.

In September 1863, a Union force of several ships returned to Bayport to destroy a blockade runner, but the Confederates set fire to it and to a cotton warehouse before the Union navy could attack.

A historical marker at Bayport Park discusses the Civil War history of Bayport. The Confederate cannon battery site can still be seen on a wooded point north of the pier at Bayport Park.

In 2009, the Florida Public Archaeology Network began a project to document and map Confederate shipwrecks at Bayport. Hernando Past, a local historic preservation society, plans to install interpretive kiosks on the Civil War at Bayport Park.

Information Provided by the Florida Department of State.