Models and modeling are central to both scientific literacy and practices as demonstrated by the Next Generation Science Standards. Through a design-based research framework, we developed a model-based assessment (MBA) and associated rubric as tools for teachers to understand and support students in their conceptualization of the flow of energy and matter within ecosystems. The MBA was piloted with four middle school students (n = 4) and implemented in two sixth grade student cohorts (n = 89 & n = 98). The MBA and rubrics went through several design iterations in order to best capture student understanding of complex systems. The design of the MBA allows students to express conceptual understanding while also capturing the transformation of their understanding as they are exposed to new information and experiences within the curricular content.