The Society for Applied Spectroscopy was selected by Kowalskis family to administer an award in Kowalskis name, the Bruce R. Kowalski Award in Chemometrics - Administered by the Society for Applied Spectroscopy, "to honor the legacy of Professor Kowalski by recognizing outstanding young researchers in the field of chemometrics and by extension, for advanced mathematical and/or statistical methods in chemistry."
The University of Washington has three scholarships set up in Kowalskis honor, the  Kowalski Excellence in Graduate Education Fund, Bruce Kowalski Endowed Fund for Graduate Student Support, and the chemistry departments Bruce R. Kowalski Endowed Fund in Chemistry.
In 2015 the American Chemical Society published a symposium series in Kowalskis honor, 40 Years of Chemometrics – From Bruce Kowalski to the Future.'
The Kowalski Prize, worth $1,000, is given annually by the Journal of Chemometrics, alternating between "the best theoretical paper and best applied paper published in the journal in the previous two years."