In this research, the authors present both the design and preliminary testing of a technology-intensive classroom intervention designed to support middle schools students' understanding of an aquatic ecosystem. The goals of their intervention are to help learners develop deep understanding of ecosystems and to use tools that make the relationships between a system's structures, behaviors, and functions explicit. This comes from data in three public middle schools in suburban school districts in the Northeastern United States. Four teachers used the instructional intervention was conducted during regular science classes. (Contains 4 figures and 2 tables.)