Rosa Smith was born on October 7, 1858 to Lucretia and Charles Kendall Smith in Monmouth, Illinois. The family moved to San Diego, California in 1876. She completed her secondary education at the Point Loma Seminary in San Diego and also attended a five-week course at a business college in San Francisco. Smith had a lifelong interest in natural history and became the first woman to be a full member of the San Diego Society of Natural History. In 1879, she met David Starr Jordan, a professor of natural history at Indiana University, who invited her to study at IU. Smith studied at IU for two years and spent the summer of 1880 touring Europe with Professor Jordan and other students and faculty from IU. Family obligations caused Smith to return to San Diego in 1882 before completing her undergraduate degree.

After returning to San Diego, Smith continued her studies of fish including the blind goby fish she discovered. She published several articles that provided formal descriptions of various species of fish. Smith also worked as a journalist and as a secretary and librarian for the San Diego Society of Natural History. While at IU, she met Carl Eigenmann who was working on his Ph.D. The two continued to correspond after she returned to San Diego, and they were married at Smith's home on August 20, 1887. The Eigenmanns often collaborated with each other on their scientific research and published numerous articles together. After their marriage, they went to Harvard University where they studied the Agassiz collections of fish. Smith was also granted special student status at Harvard to study cryptogamic botany from 1887-1888. In 1889, the Eigenmanns returned to California where they established a biological station and continued their studies of fish in the region. They also held appointments as curators at the California Academy of Sciences. Additionally, the Eigenmanns spent considerable time in South America studying and collecting freshwater fish.

In 1891, the Eigenmanns returned to Bloomington, Indiana when Carl was appointed Professor of Zoology at Indiana University. Carl was later named chair of the Department of Zoology and the first Dean of the Graduate School. The Eigenmanns had five children: Lucretia Margaretha Eigenmann, Charlotte Elizabeth Eigenmann, Theodore Smith Eigenmann, Adele Rosa Eigenmann, and Thora Marie Eigenmann. Family responsibilities prevented Rosa from continuing her own research, but she worked as an editor for her husband's papers. In 1926, the Eigenmanns left Indiana and returned to San Diego. Carl Eigenmann died on April 24, 1927. Rosa continued to live in the San Diego area until her death on January 12, 1947 of chronic myocarditis after a series of difficult eye operations.

Rosa Smith Eigenmann was one of the first women ichthyologists. Eigenmann authored twelve papers on her own and co-authored twenty-five articles with her husband. The Eigenmanns have been credited with the identification of 35 new genera of fish and descriptions of almost 150 species of fish. Additionally, Rosa Smith Eigenmann is believed to be the first woman allowed to attend graduate-level classes at Harvard University, the first woman president of IU's Sigma Xi (an honorary science society) chapter, and the first woman to determine a new species of fish.