In this paper, we share results from a classroom intervention that used a conceptual representation to support reasoning about ecosystems. Engaging students in modeling allows them to make their ideas visible while being malleable and available for discussion, which enables students to make meaning out of systems. Further, the Components-Mechanisms-Phenomena (CMP) conceptual representation was designed to enable students to construct coherent mental models. Following our intervention, students deepened their understanding of ecosystem dynamics when compared to students who engaged in traditional instruction without use of the CMP conceptual representation. We discuss our results in terms of data that helped guide the design of the intervention and we describe a theoretical perspective that can be used to guide future instruction.