In this study, we investigated how high school credit recovery students worked in small groups and used computer-based scaffolds to conduct scientific inquiry in a problem-based learning unit centered on water quality. We examined how students searched for and evaluated information from different sources, and used evidence to support their claims. Data sources included screen recordings, interviews, scaffold trace data, and scaffold entry quality ratings. Findings indicate that many students struggled to use the scaffolding and did not fully respond to scaffold prompts. Collaboration within small groups was often inhibited by frequent absences, struggles using the scaffolding, desires to complete tasks quickly rather than thoroughly, and an expectation that the group leader address the questions. However, many groups followed the scientific inquiry process prompted by the scaffolding, and support for collaboration within the scaffolds led students to negotiate the meaning of water quality data, and this in turn led students to see water quality as a complex, rather than a binary, construct.