Kujawinski was an undergraduate student at Massachusetts Institute of Technology (MIT). She was awarded the undergraduate teaching award from the Department of Chemistry. She moved to the Woods Hole Oceanographic Institution (WHOI) as a doctoral researcher, where she worked in chemical oceanography. Her doctoral research considered the effect of protozoan grazers on polychlorinated biphenyl cycling. After graduating Kujawinski joined the Ohio State University as a postdoctoral scholar.