Wakimoto's research interests include using data collected from the ground and aloft to study the evolution of severe local storms, including microbursts, thunderstorms, and tornadoes. A radar specialist, he has used airborne and ground-based Doppler radar to analyze the structure of oceanic cyclones and pollution layers as well as severe thunderstorms. A geophysicist by training, Wakimoto served as a principal investigator on a pair of landmark field projects, known as VORTEX and VORTEX2, to study tornadoes in the Great Plains and improve tornado warning systems. During the early 1980s, he participated in the first studies to identify microbursts as a threat to aviation. He became director of NCAR in 2010.
