Understanding ecosystems is challenging, but important for becoming environmentally-literate citizens of today‟s society. People have difficulty considering how different components, mechanisms, and phenomena, both visible and invisible, are interconnected within ecosystems. This research presents both the design and initial testing of an innovative and technology-intensive classroom intervention. This intervention was designed to support middle school students‟ understanding of an aquatic ecosystem through encouraging explicit Structure-Behavior-Function (SBF) conceptual representation of ecosystems. The technology support included hypermedia organized around SBF, NetLogo simulations, and an SBF modeling tool. Our study analyzed pre- and post-test data coded for SBF relationships generally, and relationships between Macro- and Micro-level (M-M) structures, behaviors, and functions, using 311 students in the classrooms of four science teachers. We found moderate to large effects of our intervention with students‟ understanding of SBF relationships and recognition of M-M level relationships increasing over time. The increased consideration of relationships derived from the SBF intervention is important for a more sophisticated understanding of ecosystems in middle school science classrooms. Additionally, by using the SBF framework, micro-level systems phenomena might be made more salient for young learners.