Promoting student understanding of ecosystem processes is critical to biological education. Yet, teaching complex life systems can be difficult because systems are dynamic and often behave in a non-linear manner. In this paper, we discuss assessment results from a middle school classroom intervention in which a conceptual representation framework is embedded in a suite of technology tools. We use both hand-drawn models and open-ended written responses to evaluate student understanding. While we speculated that our intervention would help students use ecosystem mechanisms to describe broader processes, we found instead that students tended to express constructs in isolation (as opposed to a unified picture of ecosystem processes). In addition, students provided greater elaboration of ideas mostly when specifically prompted. Specific prompts also tended to produce more accurate representations of the ecosystem processes our curriculum covered. Our findings have allowed us to refine our intervention to better translate these critical concepts, and how they are interrelated, to young learners. As such, these findings have important implications for encouraging broader ecosystem thinking in K-12 classrooms.