We describe a mobile augmented reality (AR) experience called Atom Tracker designed to help middle school students better understand the cycling of matter in ecosystems with a focus on the concept of conservation of matter and the processes of photosynthesis and respiration. Location-based AR allows students to locate virtual "hotspots," where they interact with multiple representations including vision-based AR animations of virtual atoms during ecological processes such as photosynthesis and physical LEGO® -based representations of molecules. This design case describes the design rationale, the iterative design process, the context for implementation, and reflections on the success and limitations of the Atom Tracker AR experience. An augmented reality interface was chosen due to theoretical support for its utility in supporting interaction with multiple representations (both physical and virtual) of atoms and molecules, the ability to condense and expand temporal and spatial scales associated with ecological processes, and its ability to explicitly situate these representations in real-world contexts that could support learning. Two significant design challenges that we recognized were (a) appropriately leveraging narrative, student engagement and agency when designing around the topic of atoms and molecules, which are inanimate and invisible; and (b) designing for engagement with both virtual and physical resources available during the experience