This study presents a series of three experiments that focus on how distributed scaffolding influences learners’ conceptual understanding and reasoning from combined levels of triangulation, at the interactive level (discourses within a focus group) and the collective level (class). Three inquiry lessons on plate tectonics (LPT) were designed, implemented and redesigned to explore how students responded to the scaffoldings provided. The results show that the goal-oriented version (LPT3) was significantly more effective at helping students develop an understanding of plate tectonics and evidence-based reasoning than the teacher-led (LPT1) and deconstructed (LPT2) versions (χ 2 = 11.56, p < 0.003). In LPT3, we can identify three key features of the scaffolding: an advanced organizer, deconstruction of complex tasks, and reflection on the whole inquiry cycle at the end of class time. In addition, LPT3 took much less teaching time. In other words, it appears to be effective and efficient, most likely due to synergies between teacher facilitation and lesson scaffolds. The empirical results clarify the functions of the design model proposed for distributed scaffolding: navigating inquiry, structuring tasks, supporting communication, and fostering reflection. Future studies should more closely evaluate the scaffolding system as a whole and synergies between different types of scaffolds for advancing learning.