The principal source of traffic on the railroad for many years was carrying cotton bales from Tallahassee to seaports on the St. Marks River.

The heart of Middle Florida and the adjacent part of Georgia formed the "Red Hills Region", which held many plantations producing cotton and tobacco.

Cotton bales were brought into Tallahassee, from which they were carried in wagons across the deep sand of the Woodville Karst Plain to ports on the St. Marks River.

The Legislative Council of the Territory of Florida authorized the Leon Rail-Way Company[a] in 1831 to build a railroad from Tallahassee to the St. Marks River.

Richard Keith Call, who owned two plantations in Leon County, became president and chief stockholder of the company.

As part of the proposed route crossed land still held by the Federal government, Call petitioned the U.S. Congress to grant the railroad a 200-foot (61 m) wide right-of-way, and 100 acres (40 ha) in St. Marks.

Gerstner had been commissioned by the Russian government to write a comprehensive report on railroads in the United States.

[b] By 1839, the railroad was extended two miles (3.2 km) south to Port Leon by means of a drawbridge across the St. Marks River.

The line was constructed using strap rail (eight-foot (2.4 m) long timbers with a one-half-inch (13 mm) thick strap of iron on top), using a track gauge (distance between rails) of five feet (1,524 mm) laid on ties spaced at intervals of six to seven feet (1.8 to 2.1 m).

While admitting that the railroad was "very useful" because of the near impossibility of transporting cotton by horse-drawn wagon across the sandy soil from Tallahassee to the St. Marks River, he called the railroad "the very worst that has yet been built in the entire world", with such poor construction that it had proven impossible to operate locomotives on the track.

[16][17] The Union Army and Navy mounted a raid on the area around St. Marks in March 1865 as part of an attempt to cut off peninsular Florida from the rest of the Confederacy.

Seamen and soldiers were landed at various points on Apalachee Bay in an attempt to capture or burn bridges over the Aucilla ("Ocilla" on the map), East, Ochlockonee ("Okloknee" on the map), and St. Marks rivers, to seize the towns of Newport and St. Marks, and to destroy the Tallahassee Railroad.

The main force under Brigadier General John Newton arrived at Newport to find that the bridge across the St. Marks River had been burned.

General Newton decided to cross the St. Marks on the natural bridge (where the river went briefly underground) a few miles upstream from Newport.

Confederate reinforcements, including elements of the Second Florida Cavalry, militia from Leon and Gadsden counties, and cadets from the West Florida Seminary, traveled down the Tallahassee Railroad the night of March 5 and into March 6, detraining at Hodgsons (turpentine) distillery, in the vicinity of what is now Woodville, as that was closer to the natural bridge than Newport.

Newton's forces reached the natural bridge on March 6, only to find it defended by Confederate troops.

Confederate forces held the crossing in the Battle of Natural Bridge, and the Federal troops withdrew.

A petition by the SAL to resume service to those two miles (3.2 km) to the end of the line in St. Marks was approved by the Interstate Commerce Commission in 1939.