Over the years, there has been much discussion of the use of groups to promote pupils’ academic and affective outcomes through increasing the quality of interactions in the groups. Despite the emergence of numerous group work strategies, there is concern over the integration of group work and subject teaching. In this study, a collaborative science learning environment (CSLE) is designed to help teachers incorporate small-group learning with science inquiry. The CSLE engages pupils collaboratively in an active thinking and talking process in a scaffolding inquiry cycle. The changes in pupils’ competence in science inquiry, feelings of relatedness, and the challenges faced in the CSLE were discussed.