In this paper we explore the relationship between learning gains, measured through pre‐assessment and post‐assessment, and engagement in scientific argumentation. In order to do so, this paper examines group discourse and individual learning during the implementation of NASA Classroom of the Future’s BioBLAST!® (BB) software program in a high school biology classroom. We found that the argumentative structures, the quality of these structures, and the identities that students take on during collaborative group work are critical in influencing student learning and achievement in science. We provide recommendations for instructors implementing argumentation in their science classrooms, and provide suggestions for the development of future research in this area.