Background: Research illustrates that student motivations influence learning engagement, persistence, and achievement in powerful ways and that positive motivations are linked to deeper learning, critical thinking, pro-social behavior, and better performance. Most studies of learner motivation, however, are conducted outside of STEM and are focused at the contextual level, which may describe why students attend college or choose a degree program, but not why they engage in classroom activities. Furthermore, there is little research that meaningfully connects learner motivations with gender identity and course pedagogy. This study addresses these gaps by examining the interconnections among course pedagogy, gender, and situational-level motivations, which reveal why learners engage in different course activities and how engagement may vary over time. This detailed perspective on learner motivations is essential for instructors to gain insights into how their pedagogical and course design choices influence students' motivational responses and to more effectively develop interventions that support positive forms of motivation among all students. Results: Participants in the study are undergraduate students enrolled in 72 introductory-level STEM courses across 11 institutions, and the dataset includes over 5000 unique responses to the Situational Motivation Scale, a Self-Determination Theory-based instrument that was administered weekly in each course. Analysis reveals seven typical motivational response types, ranging from a highly control-oriented to a highly autonomous response. Most students express multiple types of motivation during an academic term in a course, illustrating the dynamic nature of motivations. Cluster distributions by gender and pedagogy indicate significant differences in lecture-based learning courses, with women reporting less self-determined motivations compared to men. Motivational response profiles of women and men are both more similar, and more positive overall, in courses that employ active learning. Conclusions: These findings have important implications for practitioners. The concept of motivational co-expression encourages instructors to move toward a more nuanced appraisal of learner motivation. The stability analyses challenge embedded beliefs about the fixed nature of learner motivation. The gender analyses raise questions about how instructors may more effectively promote the positive motivations of all students through their course design decisions.