Teaching students to ask and answer questions is critically important if they are to engage in reasoned argumentation, problem-solving, and learning. This study involved 35 groups of grade 6 children from 18 classrooms in three conditions (cognitive questioning condition, community of inquiry condition, and the comparison condition) who were videotaped as they worked on specific inquiry-based science tasks. The study also involved the teachers in these classrooms who were audio-taped as they interacted with the children during these tasks. The results show that while there were no significant differences in the children's explanatory behaviour across the two time periods, there were significant differences in the total verbal interactions between the children in the cognitive questioning condition and their peers in the community of inquiry and comparison conditions. Furthermore, the children in the cognitive questioning condition obtained higher reasoning and problem-solving scores than peers in the other conditions. Interestingly, while there were no significant differences between the teachers' basic and extended mediating behaviours in the three conditions at Times 1 and 2, there was a significant difference in extended mediation behaviours with the teachers demonstrating nearly three times more extended mediation to promote students' learning at Time 2 than they did at Time 1. Teacher intervention in providing guidance in how to interact during cooperative, inquiry-based science appears to be critical to helping students engage in higher-level thinking and learning. (Contains 1 table.)