The aim of this paper is to describe the design approach developed to analyze the design and consequent activity of learners engaged in an undergraduate environmental science course. The course was taught using the EMBeRS method that emphasizes generation of external representations of mental models to build shared understanding of socio-environmental systems (Pennington et al., 2015). The design approach adopted combined expertise in (1) design research (from Sandoval, 2014) and (2) design for learning (from Carvalho & Goodyear, 2014). Taking a systems view of the design, activity, and learning outcomes, this paper describes the linkages between these and extracts the design conjectures of the instructor and the theoretical conjectures implicit in the EMBeRS approach. In collaboration with the instructor, the use of this approach: identified disconnects between design and theoretical conjectures; linked these disconnects to specific design considerations so that; recommendations for areas of redesign and parallel research were made.