Decline in student motivation is a concern for STEM education, especially for underrepresented groups in the sciences. Using the Science Motivation Questionnaire II, 41 foundational STEM courses were surveyed at the beginning and end of each semester in an academic year at a small primarily undergraduate university. Significant pre- to post-semester declines were observed in each of five measured motivational factors ("Intrinsic motivation," "Career motivation," "Self determination," "Self-efficacy," and "Grade motivation"), with effect sizes ranging from 0.21 to 0.41. However, in the second semester pre-survey, four motivational factors rebounded, including three returning to initial levels, suggesting that the observed motivational decline is not long-lasting. Analysis suggests that declines are not related to survey fatigue or student demographics, but rather to grades and, in the case of one motivational factor, to academic field. These findings suggest that a refocus on grading practices across STEM fields may influence student motivation and persistence in STEM.