After serving for three years, he became the city attorney, as well as published his first history book, Art Work of Mobile and Vicinity (1894).

His civic duties allowed him to work on his historical studies as well, so he published Colonial Mobile: An Historical Study (1897) (the first detailed relation of his native city's past, a revised edition of which was also later published), Early Southern Institutions (1898), The Colonization of the South (1904), The Reconstruction Period (1910), and Mobile of the Five Flags (1913) (a high school textbook).

Hamilton, a Democrat, was appointed as the federal judge for Puerto Rico in 1913 by President Woodrow Wilson, who was his classmate at Princeton University.

During World War I, Hamilton's wife and daughter were on a ship sunk by a German U-Boat off the New Jersey Coast, but were rescued from their lifeboat after two days.

Hamilton tried to enhance his court's public reputation and improved its administration, keeping more current with the docket than had his predecessors.

During his tenure he addressed the political status of Puerto Rico and issues relating to citizenship, and handled numerous commercial and criminal cases.

At times, Hamilton's relations with Puerto Rico's governor Arthur Yager proved tense, although President Wilson had nominated both.

That library and the Alabama Department of Archives and History were to receive his notes and research files, but a fire destroyed them before delivery.