This study examines how middle school students develop an increasingly coherent understanding of aquatic ecosystems. As part of a broader design research study that used Structure-Behavior-Function (SBF) theory as an organizing conceptual representation, we created two instructional units that focused on pond and aquarium environments. We coded and analyzed 70 middle school students' drawings of aquatic environments collected before, during, and after a technology-rich instructional intervention. Coding considered several relations between multiple system levels: Macro-Micro (MM), Biotic-Abiotic (BA), and SBF. Hierarchical Linear Modeling analysis was used to examine the relationship within and between levels. This suggested that students followed multidimensional trajectories toward an increasingly coherent understanding of aquatic ecosystems (i.e., separately across the MM, BA, and SBF dimensions). Even so, the ability to observe phenomena at multiple MM and BA levels may be an underlying constraint to observing integrated SBF relations and the development of a more coherent understanding of ecosystems. We discuss implications for instruction and the design of learning environments.