In the wake of the success of Victor Herbert's operetta Naughty Marietta in 1910, the composer sensed it was time to realize his dream of writing serious grand opera. Herbert broached the idea to theatrical impresario Oscar Hammerstein, who promptly signed a contract with Herbert for the yet unwritten work. Natoma was the brainchild of amateur librettist Joseph D. Redding (1859 - 1932), a San Francisco-based lawyer with a flair for the dramatic. Redding was a lifelong friend of Victor Herbert and when Natoma won first prize in a coast-to-coast competition for grand opera libretti, Redding contacted Herbert about making a musical setting. Although Herbert was opposed to the idea of operas based on American Indian themes, Natoma overcame his objections and he agreed to set it. Natoma, as with most of Victor Herbert's creations, was then composed in a very brief time.

Natoma is set on Santa Cruz Island in 1820, and is concerned with the selfless act of Natoma, an Indian maid in love with an American Navy Officer, Paul. Paul falls in love with Barbara, daughter of a Spanish conquistador. Natoma watches in sorrow as the romance between the two blossoms. Meanwhile, Barbara's cousin, Alejandro, who knows that Barbara will soon inherit a good-sized piece of real estate, intends to kidnap Barbara and force her to marry him. Natoma foils this plot as it gets underway by driving her dagger into Alejandro's chest. Natoma resigns herself to a life of contrition in a monastery, as Paul and Barbara go away to marry.

From the very start the production was plagued with problems. Oscar Hammerstein was to mount the first performance, but as the score was completed Hammerstein's fortunes were in a down cycle and he had already lost his theater, the Manhattan Opera House. Natoma was instead diverted to Philadelphia, where it debuted on February 25, 1911. On February 28, Natoma was repeated with the same cast, mostly ex-members of the Manhattan Opera Company, at the Metropolitan Opera in New York. Mary Garden portrayed the title role, and the young Irish tenor John MacCormack made his opera debut creating the role of the American seaman Paul. It would also mark MacCormack's last appearance in a staged opera; he was a recitalist, not an actor, and discovered this shortcoming as a result of his experience in Natoma.

Victor Herbert's music for Natoma was naturally delightful, and two instrumental bits of the opera, the Habanera and Dagger Dance, persisted as light classical favorites for quite some time after the opera itself disappeared from view. Upon its New York opening the critics were brutal, and the work has seldom been revived since 1911. John MacCormack's own summary of Natoma is terse, but states the basic facts very well: "Herbert was a great master of operetta, and I always feel that Natoma was an overgrown operetta, one that had grown bigger and more bombastic."

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