Originally built by Henry Flagler as part of the Overseas Railroad, construction began in 1905 and was completed in 1912. Operated by Flagler's Florida East Coast Railway, which ran the entire length of the east coast of Florida, the Overseas Railroad was a single rail track extension linking Key West to mainland Florida.
Due to the Bahia Honda channel depth, being 24-feet at it’s deepest point, the Bahia Honda Bridge was built with a steel truss construction, instead of a concrete arch form that was used throughout the rest Overseas Railway.

The Overseas Railroad met its demise when the Labor Day Hurricane of 1935, a Category 5 hurricane often referred to as "The Storm of the Century", where more than 400 lost their lives and devastated many of The Keys. In an attempt to evacuate, an FEC rescue train which was overturned by the storm surge at Islamorada, with the exception of steam locomotive 447. Over 40 miles of track were washed away by the hurricane, two miles of which washed ashore on the mainland at Cape Sable. The Florida East Coast Railway, already bankrupt, was financially unable to rebuild the destroyed sections. The roadbed and remaining bridges were sold to the State of Florida, which built the Overseas Highway to Key West, using much of the remaining railway infrastructure. Many of the original bridges were replaced during the 1980s. The Overseas Highway continues to provide a highway link to Key West.

The Overseas Highway was added to the National Register of Historic Places in 1979 as Overseas Highway and Railway Bridges. To this day the original Bahia Honda bridge remains still stand, however it has fallen into a state of disrepair, with signs warning boaters of falling debris. The easternmost section of the bridge is open to the public and offers a panoramic view of the area and near by keys.