He studied medicine at Albany, and after taking his degree practised for some years in Berkshire county. His interest in geology was kindled in early life, and in 1824 he had assisted Prof Chester Dewey (1784-1867) in preparing a geological map of Berkshire county, in which the first attempt was made to classify the rocks of the Taconic area. He still longed to pursue his interest in geology, so decided to attend the Rensselaer School (now RPI). There, he was inspired by the eminent professor Amos Eaton, and graduated from Rensselaer in its first class in 1826. While thus giving much of his time to natural science, undertaking professional work in natural history and geology in Williams College, he also accepted the professorship of chemistry and afterwards of obstetrics at Albany Medical College.
The chief work of his life was, however, in geology, and he has been designated by Jules Marcou as the founder of American palaeozoic stratigraphy, and the first discoverer of the primordial fauna in any country. In 1836 he became attached to the Geological Survey of the State of New York, and after lengthened study he grouped the local strata (1842) into the Taconic and overlying New York systems. The latter system was subdivided into several groups that were by no means well defined. Emmons had previously described the Potsdam sandstone (1838), and this was placed at the base of the New York system. It is now regarded as Upper Cambrian.
In 1844 Emmons for the first time obtained fossils in his Taconic system: a notable discovery because the species obtained were found to differ from all then-known Palaeozoic fossils, and they were regarded as representing the primordial group. Marcou was thus led to advocate that the term Taconic be generally adopted in place of Cambrian. Nevertheless, the Taconic fauna of Emmons proved to include only the lower part of Sedgwick's Cambrian.
Emmons made contributions on agriculture and geology to a series of volumes on the Natural History of New York (1848). He also issued a work entitled American Geology, containing a statement of the principles of the science with full illustrations of the characteristic American fossils (1855-1857). From 1851 to 1860 he was state geologist of North Carolina. He died at Brunswick, North Carolina, on the 1st of October 1863.
The overthrust in New York which places Lower Cambrian rocks in contact with Middle Ordovician rocks is named for him, known as Emmons' line, formerly Logan's line. It is a segment that extends from Canada through Vermont, New York, and farther south. It traverses through the city of Troy, New York and the Poestenkill Falls and Gorge. He named the Adirondack Mountains (1838) and Taconic Mountains (1844) and acquainted the public with these regions.