The Indianola Railroad Company was chartered on January 21, 1858, to build from the port of Indianola at Powderhorn Bayou on Matagorda Bay fifteen miles to a connection with the San Antonio and Mexican Gulf Railroad at Clark Station in Calhoun County. The SA&MG had begun construction at Port Lavaca in 1856, its avowed destination being Victoria and San Antonio. By January 31, 1858, the SA&MG had laid only five miles of track to Clark. It reached Victoria in April 1861. Alarmed by the success of their rival port in getting a railroad under way, Indianolans secured the charter for the Indianola Railroad Company to protect their commercial interests. Authorized capital was $5 million. Sale of stock to local investors raised the necessary funds to permit grading of the fifteen-mile-long roadbed to Clark Station and the purchase of ties, which were stacked on the beach at Indianola. When Wilhelm C. A. Thielepape laid out Brown's Addition at Powderhorn Bayou, he also surveyed a railroad route between Powderhorn and Chocolate bayous. It was utilized later as the right-of-way for the Indianola Railroad. The road had trouble securing American financial backing to complete construction and purchase rolling stock. In large measure, that failure was attributable to nervousness in financial markets of the North about the possibility of impending civil conflict. The directors turned to Europe. In addition to Henry Runge, president, the board then consisted of William H. Woodward, John E. Garey, H. J. Huck, John H. Dale, and David C. Proctor. Runge traveled to Germany in 1860 to interest investors in the planned railroad; however, the acts of secession brought all such activities to a halt. The plan remained in limbo until after the Civil War. In December 1862, as part of a "scorched earth" policy, Confederate forces, acting on order from Gen. John Bankhead Magruder burned the stock of railroad ties, an estimated 750,000 boardfeet of lumber, at Indianola. The Confederate Army also partially wrecked the SA&MG track from Port Lavaca to Victoria to prevent its use by anticipated Union invaders.
On October 19, 1866, the Texas legislature renewed the charter of the Indianola Railroad Company and extended the required completion date to Clark Station to January 1, 1871. Work resumed in 1869. Thirteen miles of chair-iron rails was laid. A freight and passenger depot, which held the headquarters office, and car and locomotive shops were erected at Indianola. Construction costs in excess of funds on hand soon stopped the work again. Steamship-line owner Charles Morgan of New York began buying into the Indianola Railroad Company until he secured a majority interest. Morgan also purchased Water lots C1 and C2, Wharf Lot C, and building lots on Travis Street, onto which the railroad curved toward the long wharf that was built out into Matagorda Bay at the foot of Travis. Rails were laid on the wharf so direct transfer of goods could be made between vessels and railroad freight cars to reduce labor costs. The Indianola Railroad track was changed in 1870 from its original wide gauge of five feet, six inches to the standard gauge of four feet, eight and one-half inches. That necessitated altering the length of axles on rolling stock. The gap of two miles to the junction with the SA&MG at Clark Station was closed in April 1871. Morgan and his business partner, Henry S. McComb, had purchased the SA&MG at the United States government foreclosure sale in 1870, paying off the indebtedness to the United States for the cost of rebuilding in 1865–66. At a meeting in Indianola on April 22, 1871, Morgan took steps to consolidate the Indianola Railroad Company with the SA&MG, forming a new corporation to be known as the Gulf, Western Texas and Pacific Railway Company. Legislative approval of the consolidation was given on May 19, 1871. In 1873 the line was extended from Victoria to Cuero; however, the financial panic of that year halted planned construction to San Antonio. Cuero remained the inland terminus of the GWT&P. Catastrophic damage to railroad property on the bay was caused by the Indianola hurricane of September 16, 1875, which wrecked Indianola and caused great loss of life. The GWT&P tracks were taken up from Clark Station to Port Lavaca, but service continued from Indianola through Victoria to Cuero. As a result of the disastrous hurricane of August 20, 1886, and the destruction of Indianola (including the railroad's long wharf, shops, and depot complex), that town was abandoned the following year as the bay terminus of the GWT&P. Legislative approval was granted for removal of the rail line from Indianola to Clark Station and rebuilding of the track from that junction to Port Lavaca. The final train from Cuero to Indianola, an excursion, ran on June 18, 1887. Service to Port Lavaca on the reconstructed track from Clark began on November 5, 1887.