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Our study aims to develop a set of criteria for the three-dimensional assessment of students’ construction of explanatory models on the impact of ocean acidification (OA) on oyster larvae. Our data source is 152 explanatory models that were created by groups of students from 22 classrooms in different secondary schools. Our MultiModal Discourse Analysis shows that explanatory models can make explicit students’ alternative conceptions, systems thinking in regards to climate change impacts, choices of scientific representations, and the ways they integrate evidence within their explanatory models. We suggest explanatory models as powerful tools that shed light on the process of students’ ideas and epistemic commitments on the complex and interdisciplinary topic of climate change.