Emerson attended Amherst College, where he joined the Alpha Delta Phi fraternity and from which he graduated in 1865 as valedictorian. He went on to study in Germany at the University of Berlin, and received his doctorate from the University of Göttingen in 1870. He returned to the United States where he joined the faculty at Amherst, where he was professor of geology and related sciences from 1872 to 1917 and simultaneously at Smith College from 1878 to 1912. He was also assistant geologist from 1890 to 1896, and later geologist from 1896 to 1920 for the United States Geological Survey. He helped found the Geological Society of America and was its president in 1899.