Classroom discourse can affect various aspects of student learning in science. The present study examines interactions between classroom discourse, specifically teacher questioning, and related student cognitive engagement in middle school science. Observations were conducted throughout the school year in 10 middle school science classrooms using the Electronic Quality of Inquiry Protocol, which is designed, among other things, to measure observable aspects of student cognitive engagement and discourse factors during science instruction. Results from these observations indicate positive correlations between students' cognitive engagement and the following aspects of classroom discourse: questioning level, complexity of questions, questioning ecology, communication patterns, and classroom interactions. A sequential explanatory mixed-methods design provides a detailed look at each aspect of classroom discourse which showed a positive effect on student cognitive level during science instruction. Implications for classroom practice, teacher education, and professional development are discussed.