Argumentation enables students to engage in real world scientific practices by rationalizing claims grounded in supporting evidence. Student engagement in scientific argumentation activates the negotiation process by which students develop and defend evidence‐based claims. Little is known, however, on the intricate process and potential patterns of negotiation between students during scientific argumentation. The present study seeks to fill this gap by exploring how a group of university science education students negotiated when evaluating the relationship between lines of evidence and alternative explanatory models of a phenomena (i.e., climate change). This research, theoretically grounded in social constructionism, used Halliday's model of Systemic Functional Linguistics (SFL) within a discourse analysis framework. The authors analyzed transcripts of student conversations during a model‐evidence link activity to gain insights into patterns of negotiation. An interpersonal analysis centering on mood and moves revealed students' ability to engage in the negotiation component of scientific argumentation to make assertions about relations between evidence and models. Effective collaboration resulting in group consensus of the relationship (categorized as supports, strongly supports, or contradicts) was facilitated by the use of interrogatives, modulation, and a balanced contribution between group members. Conversely, negotiation which did not reach consensus featured less balanced discussion among group members, contained more interruptions, more conflict moves, and double polarity clauses.