This study examines the ideas students generated during an online inquiry investigation and how students used these ideas to construct scientific explanations about everyday phenomena. We designed and implemented a four-day, technology-enhanced inquiry unit on the chemistry of recycling with 164 high school students. The unit incorporates the Idea Manager, a new inquiry scaffolding technology that helps students record their ideas and construct coherent explanations. We scored the conceptual content of the ideas students recorded, how students organized their ideas, and the coherence of students' explanations. Regression models show that students' ability to distinguish ideas predicted explanation coherence more strongly than the number of relevant ideas they recorded. Three cases illustrate difficulties some students had using molecular concepts to support their explanations. The findings demonstrate how this new technology can permit closer examination of students' learning progress and inform curricular refinements.