Cooper served two terms in the state Senate, from 1880 to 1884, and was president pro tem during his second term. He wrote a bill granting each Confederate veteran 1,280 acres of state land. In 1885 President Grover Cleveland named him collector of internal revenue at Galveston, a position he held until 1888. Cooper ran unsuccessfully for district judge in 1889 but was elected in the Second Texas District to the first of six consecutive terms in the United States House of Representatives in 1892. He was defeated by Moses L. Broocks in 1904 but came back to beat Broocks in 1906 for a position in the Sixtieth Congress, only to lose to Martin Dies in the 1908 race. While a member of the Congress, Cooper served on the House Ways and Means Committee. He helped secure $600,000 in federal appropriations to link Beaumont with the Port Arthur ship channel. With Cooper's support, a nine-foot-deep channel was dug in 1908; later improvements tied Beaumont to the Sabine-Neches Waterway and made the city a deepwater port.
Cooper was chairman of the Texas delegation to the Democratic convention in Kansas City (1904). In 1910 President William Howard Taft appointed him to the Board of General Appraisers, a customs court that sat at New York. Cooper was affiliated with the Masonic lodge, the Independent Order of Odd Fellows, the Knights of Pythias, and the Benevolent and Protective Order of Elks. He died in New York on August 21, 1918, after a short illness. His funeral and burial were in Beaumont. He was survived by four of his five children, his wife having died in 1911. One of his daughters, William (Willie) Chapman Cooper, married William P. Hobby, and another married S.W. Sholars, congressman from Tyler County.
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