To learn and reason effectively about complex phenomena, a central goal in education, learners need opportunities to engage with them. Technology-mediated learning environment, such as simulations, can provide opportunities for learners to formulate, test, refine, and repair their mental models of complex systems. However, technology tools do not stand alone - they are situated in complex learning environments that require consideration of learning at the level of the individual, small group and whole class, as well as consideration of the roles that both the teacher and technology play in scaffolding student learning. While technology can enable the development of rich learning environments, the extent to which and how this technology can be used by teachers and how it influences the nature of student´s collaborative knowledge construction is still unclear. Appropriate analytical tools are needed to represent students´ mediated interactions in computer-supported collaborative learning (CSCL) environments. In this chapter, we present analytical tools that help us construct a comprehensive picture of how learning is mediated over time through a complex interplay of tool use, teacher scaffolding, and collaborative discourse to investigate the mediating roles of technology and teacher and peer scaffolding in CSCL. In particular, we will show how different representations (e.g., CORDTRA diagrams) can provide insight into the complexity of understanding of complex CSCL learning environments.