Educational research continues to reiterate the need for inquiry-based instruction in secondary science. However, the patterns of how teachers implement inquiry-based pedagogy have not been thoroughly studied--particularly from a quantitative perspective. This study is based on data from 422 observations of 50 teachers collected during a 5-year professional development program using an observation protocol (Electronic Quality of Inquiry Protocol [EQUIP]) designed to measure the quality of inquiry-based instruction. We focused on the relationships between teacher facilitation of inquiry, student cognitive engagement, and components of inquiry, as measured by EQUIP. Using the scores from EQUIP, we developed models using growth curve modeling to illustrate the lesson patterns of student cognitive engagement as influenced by teacher practice and components of inquiry. Our final model suggests that the strongest predictor of student engagement is teacher activity in facilitating inquiry and that growth is significant for teachers starting at low-level practice and nonsignificant for teachers starting with high-level practice, proficient or above. This model, which accounts for 74% of the total variance found, also demonstrates a significant positive association between student cognitive activity and the Engage and Explain phases of the inquiry cycle, a nonsignificant association with the Explore phase, and a negative association with the Extend phase. Our model suggests that professional development for teachers focused on specific components of inquiry may help teachers facilitate higher student cognitive engagement.