This is an exploratory study about how middle school students develop an increasingly coherent understanding of ecosystems. As part of a broader design research program, we coded and analyzed 12 middle school students’ drawings of aquatic environments collected before, during, and after a technology-rich instructional intervention. Coding considered several dimensions: relations (macro/micro, biotic/abiotic, structure- behavior-function) as well as coherence, and extraneous structures. Findings suggest that students may follow multiple non-linear trajectories towards an increasingly coherent understanding of ecosystems. Even so, the ability to observe phenomena at multiple macro/micro and biotic/abiotic levels may be an underlying constraint to also observing integrated structure-behavior-function relations and the development of a more coherent understanding of ecosystems.