His research has focused primarily on ocean ecology; he has also worked in biomedical applications. In the realm of ocean ecology, several acoustic systems invented by Jaffe resulted in the first ever behavioral observations of zooplankton in situ. In addition, the small-scale distribution of phytoplankton, as mapped via an autonomously deployed imaging fluorometer, have provided unprecedented views of oceanic biota. A new generation of miniature, sensor-equipped drifters that can acoustically network is also being considered in order to gain insights into coastal circulation and larval transport. Most recently, Jaffe is developing underwater microscopes for in-situ characterization of micro and macro plankton.
The National Science Foundation, the Office of Naval Research, California Sea Grant, the U.S. Army Breast Cancer Research Program, and the Seaver Institute of Los Angeles, and the W. M. F. Keck Founcation of Los Angeles have supported his research.