[citation needed] She moved to the Woods Hole Oceanographic Institution (WHOI) as a doctoral researcher, where she worked in chemical oceanography.
[citation needed] Kujawinski joined the faculty at Barnard College in 2002, and held an adjunct position at Columbia University.
[6] She makes use of high-resolution mass spectrometry and automated high through-put methods to analyze the low molecular waste organic materials in seawater.
[9] She works alongside the Bermuda Institute of Ocean Sciences to establish which chemical compounds are produced by microorganisms.
[11][12] Kujawinski was appointed Director of the National Science Foundation Center for Chemical Currencies of a Microbial Planet in 2021.