In 1866 Stewart moved to Houston, where he practiced law with D.U. Barziza, J.B. Likens, and G.H. Breaker. Stewart gained recognition as both a civil and a criminal attorney. An important part of his civil practice involved land litigation and suits against railroads. He served as Houston city attorney from 1874 to 1876. In 1878 he was elected to the Texas Senate, where he was an advocate of tax-supported public education. After one term in the Senate (1879-72), Stewart was elected as a Democrat to the United States Congress, where he served five terms (1883-93). In Washington, Stewart was a member of the Committee on Rivers and Harbors and worked for increased appropriations for harbor improvements on the Texas coast. He also advocated securing a railroad link between the United States and Argentina in order to increase United States exports to Central and South America. Stewart belonged to various Masonic bodies and in 1883 served as grand master of Masons in Texas. In 1892 he declined to run for office again. He returned to Houston, where he practiced law with his son, John S. Stewart. After several years of failing health, Stewart died of phthisis and diabetes in Santa Rosa Hospital in San Antonio on September 21, 1895, and was buried in Glenwood Cemetery, Houston. His son, who was city attorney at the time of Stewart's death, was his only surviving child.
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