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Within an inquiry-based lesson, science students progress through a cycle of activities leading to meaningful development of understanding of a concept. However, in a typical inquiry class students may be more or less cognitively engaged in particular components of the inquiry cycle—a conjecture that has not been addressed by existing research. This work uses data from a 5-year professional development program to develop models of how student engagement fluctuates during the inquiry cycle. We use growth curve modeling to show that patterns do exist, and that they differ depending on teacher activity to facilitate inquiry. These patterns suggest areas in need of more substantial focus from science teacher educators.