This study examined how differing instructional scaffolding influenced the actual use of evaluation skills to improve argumentation quality during college science inquiry. Source representation scaffolds supported multi-faceted reflection of complex source properties while managing cognitive load. Students were given an online annotation tool (treatment) in addition to a checklist (control). Goal instructions intended to induce critical task perceptions and evaluation standards. Balanced reasoning goals (treatment) replaced a typical persuasion goal (control). Students from one introductory biology course were assigned to one of the two by two combinations, which was implemented over one academic semester. We examined student arguments during and after interventions respectively to measure evidence quality, reasoning, and conceptual integration. Overall, scaffolds did not influence argumentation independently; rather we detected complex interaction effects across scaffolds and classroom dynamics. For low-prior knowledge groups, annotation increased argumentation quality when complemented by balanced goals. For mixed-prior knowledge groups, annotation alone impacted on argumentation independent of goal instructions. Transfer effects were marginal yet promising for low-prior knowledge groups. The results supported the synergistic integration of two scaffolding functionality, yet suggested possible difficulties in using and sustaining scaffold effects in complex classroom situations.