Born in Council, Idaho, and educated at the California Institute of Technology, Rainwater went on to gain his BS, MA, and PhD from Columbia University. At Columbia he progressed through physics assistant (1939–42), to instructor (1946), assistant professor (1947), and associate professor (1949), to become full professor of physics in 1952. In the intervening years of World War II he worked for the Office of Scientific Research and Development and on the Manhattan (atom bomb) project.

Rainwater's principal academic achievement was in explaining the structure and behavior of the atomic nucleus. At the time, two independent models existed, each explaining some of the properties of the atom – the ‘shell’ model of independent particles, and the ‘liquid-drop’ model of collective motion. Rainwater, in collaboration with Aage Bohr, showed how these theories could be unified (1950).

Rainwater, Bohr, and Benjamin Mottelson (Bohr's principal collaborator in Denmark) are credited with developing a unified theory that reconciled the individual motions of the nuclear particles with the collective behavior of the nucleus. For this the three men shared the 1975 Nobel Prize for physics.

From 1951 until 1953 and again in the period 1956–61, Rainwater was director of the Nevis Cyclotron Laboratory. From 1965 he spent much of his time supervising the conversion of the synchrocyclotron there.