In 1972 he joined the chemistry faculty at Colorado State University as an assistant professor. He moved to the University of Washington in 1974 where he stayed until his retirement in 1999. He became a full professor in 1979 and an endowed professor of analytical chemistry in 1991. The chemistry departments newsletter, Chem Letter, reported that ten companies contributed to the endowment and that it was the first endowed professorship at the university "established through a consortium of industrial and state resources." Former graduate student David Duewer summarized Kowalskis accomplishments in the Journal of Chemometrics: "32 PhD and three MS students, over 230 research publications, editorials, chapters, and reports (32 in this journal) with 144 coauthors, more than 230 invited lectures, four patents, more than 50 quarters of undergrad and graduate sections spread over 18 courses, more than $22m in grants, and – not least – founder of this journal."