Willauer started researching biphasic systems and phase transitions after graduating from Berry College. In 1998 she studied aqueous biphasic systems (ABS) for the potential of recapturing valuable dyes from textile manufacturing effluent. She investigated ions and catalysts.
In the 2000s, Willauer began studying methods for extracting CO and H from seawater, for the purpose of reacting these molecules into hydrocarbons by using the Fischer–Tropsch process. She also investigated modified iron (Fe) catalysts and studied zeolite (nanoporous aluminosilicate) catalyst supports for recombining these molecules into jet fuel.
Previous studies had concluded that CO, under the form of the bicarbonate anion (HCO) dominant (96% mole fraction) in the seawater inorganic carbon species could not be economically removed from seawater. However, by acidifying seawater by means of an adapted electrolysis cell with cation permeable membranes (dubbed a three-chambered electrochemical acidification cell), it is possible to economically convert HCO into CO at a pH lower than 6 and to increase the extraction yield. In January 2011, the NRL installed a prototype of seawater electrolysis cell at Naval Air Station Key West in Florida.
In 2017, Willauer et al. were granted a patent for a  extraction device from seawater, in the form of an electrolytic-cation exchange module (E-CEM). The E-CEM is seen as a "key step" in the production of synthetic fuel from seawater. Other researchers named in the patent are Felice DiMascio, Dennis R. Hardy, Jeffrey Baldwin, Matthew Bradley, James Morris, Ramagopal Ananth and Frederick W. Williams.