University instructors are challenged to involve large student populations with varying pre-existing knowledge in authentic inquiry. We present a model in which students collaborate to design and run their own experiment and engage in peer evaluation. In the model, students in different lab sections of a multi-section course explore alternative interconnected hypotheses based around a common theme. A pooled data set from the multiple sections then forms the basis for discussion during an interactive lecture session. This experience has a significant impact on student confidence towards participation in science, and establishes a model for enhanced skill development. To demonstrate the approach, we provide a case study that explores the relationships between leaf degradation, microbial colonisation and macroinvertebrate feeding in a stream ecosystem.