At the age of fifteen he emigrated to New York and found work there as a clerk. In 1833 he went to Charleston, S. C. , and was employed first as a bookkeeper, and later as a real-estate agent. He also had a newspaper and cigar agency and became a notary public. There was a considerable German population in Charleston and South Carolina, and Wagener was a leader in a movement for its economic and social improvement. A partial list of the organizations which he founded or promoted bears witness to his unusual initiative and energy: the German Fire Company of Charleston, 1838, of which he was president until 1850; the German Evangelistic Congregation, 1840, of which he was acting pastor for a time; the Teutonic Union for the promotion of German literature, song, and education, 1843; Der Teutone, 1844, a biweekly periodical, with Wagener as editor; the Athletic Union, a German amateur theatre, 1846; the Carolina Mutual Fire Insurance Company, 1851, of which he was president until his death; Deutsche Ansiedlungs-Gesellschaft von Charleston, 1855; and Brederlicher Bund, 1856. On October 6, 1848, at Wagener's suggestion, the German Colony Society was founded, and in the following year the town of Walhalla was established on a beautiful site in the uplands of the state in Oconee County. Of all his achievements he took greatest pride in this. Soon after his arrival in Charleston he had joined several German military organizations and was gradually advanced in rank; he became lieutenant of the German Riflemen in 1836; first lieutenant, German Fusileers, 1843; and captain, German Artillery, 1847. In 1860 he was appointed major of the 16t Artillery Regiment of the South Carolina militia. In July of the following year he was promoted lieutenant-colonel, and in September, colonel, with orders to proceed to Port Royal, S. C. Here he built and commanded Fort Walker and participated in the battle of November 7, in which he was wounded. On December 7, 1861, the South Carolina General Assembly adopted a resolution thanking him and the German battalion for their conspicuous gallantry. After recovering from his wound he returned to his command, which was employed in the defense of Charleston. In 1866 the reconstruction governor appointed him brigadier-general of the 4th Brigade of the state militia. Wagener's war services strongly recommended him for political preferment, and in 1866 he was elected to the legislature. In 1867 the governor chose him to head the newly created office of commissioner of immigration, a position for which he was well fitted by reason of his special knowledge and interest. As commissioner he published in the English, German, and Scandinavian languages an attractive pamphlet entitled South Carolina: A Home for the Industrious Immigrant (1867), and listed more than three hundred thousand acres of vacant land. Since the Negroes and poor whites opposed immigration, the office was abolished in 1868. Three years later Wagener was a fusion candidate for mayor of Charleston on the Citizens' Conservative ticket and was elected, with a majority of 777 votes. A candidate for reelection in 1873 and 1875, he was opposed by many dissatisfied conservatives and was defeated. His friends claimed that he was "counted out"; his enemies said he was ambitious to be governor. His views on behalf of the colored portion of the population were not popular with many of the white people. Early in life Wagener wrote an amateurish novel, Der Seminolenferst, which was published in the German press, and he also had a reputation as a local poet. To Der Deutsche Pionier, a periodical of the German Pioneer Club of Cincinnati, he contributed various sketches relating to the history of the Germans in the South, and at the time of his death he was collecting materials for a history of the German participation in the Civil War on the Southern side. He served at the head of the South Carolina Democratic electoral ticket for 1876 until his death that year. This occurred at his much-loved Walhalla, from dropsy. The final interment was at Charleston.
On June 28, 1837, he married in Charleston Marie Elise Wagner, who bore him nine children - Henry, Julius, Albertina, Thusnelda, Emile, Andreas, Hancke, Louisa, and one other. Two of his sons were in the Confederate army.