Bowles inherited the Republican from his father, Samuel Bowles (II) (1797-1851), who had established the paper as a weekly in 1824. When Bowles, the younger, took over, he first converted the paper to an evening daily and later to a morning journal. Bowles was highly involved in all aspects of the paper's operations and retained primary editorial control for most of his career. During his tenure, the paper gained a national reputation, though it remained largely regional and local in its concerns, featuring news from Springfield and surrounding small towns. At the time, the New York Tribune called it "the best and ablest country journal published on the continent. In 1857 Bowles attempted to expand into the Boston market by partnering to publish the Boston Traveller. As the new venture was largely unsuccessful, he left the partnership after a few months to return as editor of the Republican.
Alongside its news items, the Republican published sermons, poetry, short fiction, and took a strong moral and political editorial stance. During the controversies affecting slavery and resulting in the American Civil War, Bowles's paper supported, in general, the Whig and Republican parties and an anti-slavery agenda. In the period of Reconstruction under President Grant, his paper represented anti-administration or Liberal Republican opinions. In the disputed election of 1876 he favored the claims of Samuel J. Tilden, the reform candidate who won the popular vote but lost the Electoral College. Subsequently, the paper became independent in politics.
The long-running success of Bowles's paper was attributed not only to its subject matter and local relevancy but also to its lively, concise, and professionally written style. George S. Merriam in his Life and Times of Samuel Bowles (1885) described Bowles's style in the following way:
His style was admirable,--simple, direct, pure, forcible without being passionate, pungent without being vulgar, often delicately sarcastic and deliciously humorous, never egotistical, never suggesting the writer, always representing the journal, and this as the voice of the people,--he was by nature, by culture, by experience the model modern working journalist. He saw the world without, partly through others, but chiefly through its own words, interpreted to him by his own divine instincts. (107)
During his lifetime, Bowles published two books of travel, Across the Continent (1865) and The Switzerland of America (1869), which were combined into one volume under the title Our New West (1869). While an author himself, Bowles was friends with notable men and women of American letters. Josiah Gilbert Holland, a novelist and poet, was both a friend to Bowles and an associate of the Republican. Bowles was also a close friend and correspondent with the poet Emily Dickinson and her family. It has been speculated that he is the subject of Dickinson's erotic and submissive "Master" letters, though this is debated among scholars.
In 1848 Bowles married Mary Schermerhorn, and together they had several children. Bowles died in Springfield in 1878, and he was succeeded as publisher and editor-in-chief of the Republican by his son Samuel Bowles (IV) (1851-1915). Samuel Bowles (IV) married Elizabeth Hoar, the daughter of Ebenezer R. Hoar and niece of George Frisbie Hoar.