- Bicentennial Medal (2020)
- President's Award for Distinguished Teaching (1998)
Recalls one former student of Sklarski, "Her interest and joy of the subject matter were so complete and so infectious that everyone was engaged. She was often really humorous. She once drew with eyeliner all over her face, making theatrical expressions to explain the facial muscles. She would circle the class, always exhorting and talking, keeping everyone in earnest concentration." Another former student wrote, "Now working in Maine, I feel Bonnie's presence in my own studio: when my work lacks rigor or ambition I conjure up her imagined disapproval. She is an artist of the highest standards who has no patience for facile solutions or styles which mask a lack of substance. When I produce something of value, I want to share it with her."
In 2020, Sklarski received Indiana University's Bicentennial Medal in recognition of her distinguished contributions to the university.