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Engaging students in epistemic and conceptual aspects of modeling practices is crucial for phenomena-based learning in science classrooms. However, many students and teachers still struggle to actualize the reformed vision of the modeling practice in their classrooms. Through a discourse analysis of 150 students’ explanatory models (as social semiotic spaces) from 14 classes, we propose a qualitative framework that investigates conceptual coherence and epistemic discourses to achieve a gapless explanation of scientific phenomena. Our framework draws attention to four critical components of students’ explanatory models: (a) key ideas based on evidence, (b) the discourse modalities of how evidence is presented, (c) scientific representations from the cultures of scientific disciplines, (d) systems thinking approaches directly and indirectly related to oceans and marine ecosystems. Our results indicate that students struggled to construct cohesive explanatory models that communicated all key ideas and the relationships among them, with the majority of student-developed models in our study categorized as ‘insufficiently’ cohesive (lacking key ideas and the relationships among them), and only a small percentage of the models considered ‘extensively’ cohesive (all key ideas attended to, as well as the relationships among them).