In this study we address the need to promote student engagement with school science and the need to measure a more comprehensive conception of engagement considering three dimensions of engagement: emotional, behavioural, and cognitive. We address the first issue by designing and implementing a model-based inquiry instructional sequence focused on fostering students' engagement with science. The second issue is addressed by developing and testing a heuristic that measures student engagement holistically by focusing on all three dimensions mentioned. The results report that our short MBI instructional sequence develop students' emotional engagement because most of them recognize to having felt interest, concentration, and satisfaction and few students reported boredom, shame, or rejection during the teaching. They spent most of the time working in small groups and sharing-discussing their hypothesis, planning and evaluating their experimental designs, and building models to explain acid-base phenomena together which highlight behavioural and cognitive dimension of students' engagement in our instructional sequence about chewing gum and pH of the mouth. The heuristic is designed to gather data continuously during instruction with minimal disruption to the learning and teaching sequence. The heuristic can be used by teachers, researchers, and also by students, to gain multi-level understandings about engagement by focusing on individual, group-level, or class-level analysis of responses.