Teaching science inquiry practices, especially the more contemporary ones, such as computational thinking practices, requires designing newer learning environments and appropriate pedagogical scaffolds. Using such learning environments, when students construct knowledge about disciplinary ideas using inquiry practices, it is important that they make connections between the two. We call such connections epistemic connections, which are about constructing knowledge using science inquiry practices. In this paper, we discuss the design of a computational thinking integrated biology unit as an Emergent Systems Microworlds (ESM) based curriculum. Using Epistemic Network Analysis, we investigate how the design of unit support students’ learning through making epistemic connections. We also analyze the teacher’s pedagogical scaffolding moves that support such connections. This work implies that to support students’ epistemic connections between science inquiry practices and disciplinary ideas, it is critical to design restructured learning environments like ESMs, aligned curricular activities and provide appropriate pedagogical scaffolds.