This design case details the design process of a multiple-choice assessment of socio-scientific systems thinking. This assessment is situated within a larger project that aims to understand the ways students use multiple scientific models to understand complex socio-scientific issues. In addition to the research component, this project entails developing curriculum and assessment resources that support science teaching and learning. We begin this paper by framing the needs that motivated the design of this assessment and introducing the design team. We then present a narrative outlining the design process, focusing on key challenges that arose and the ways these challenges influenced our final design. We conclude this paper with a discussion of the compromises that had to be made in the process of designing this instrument.