He then served as a surgeon for United States Army during the War of 1812, stationed in New Orleans, Louisiana, then Natchez, Mississippi, before resigning there into private practice.

In Mississippi, Mercer owned four plantations in Adams County—Laurel Hill, Buckhurst, Ellis Cliffs, and Ormond—and property in Coahoma County.

[citation needed] He was a member of Christ Church Cathedral and president of St. Anna’s Asylum in New Orleans.

[6] Mercer was the President of the Board of University of Louisiana under with Secretary Albert G. Blanchard, Chief Justice of the Louisiana Supreme Court Edwin T. Merrick, Mayor of New Orleans Charles M. Waterman (politician), Admin Pierre Emile Bonford, Admin.

[8][9] The family resided at their Laurel Hill Plantation in Adams County, where Mercer built St. Mary's Episcopal Chapel.