Considering well-documented difficulties in mastering ecology concepts and system thinking, the aim of the study was to examine 9th graders' understanding of the complex, multilevel, systemic construct of feeding relations, nested within a larger system of a live model. Fifty students interacted with the model and manipulated a variable within it in the course of this model ecosystem yearlong inquiry, in a laboratory/traditional learning environment. Students' written responses to 10 pretest-posttest probes underwent fine-grain analysis regarding 53 descriptors of the system of feeding relations. Overall, students exhibited initial system thinking, manifested in different levels of increased ability to identify: system components, processes, levels, and their interrelations; ecosystem patterns and control mechanisms; equilibrium shifts; and spatial and temporal aspects of feeding relations. However, many still exhibited a deficient understanding of the system studied, reflecting a deficient system thinking. Implications for systemic ecology teaching and learning are discussed.