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The development of student epistemic agency is a vitally important goal for science education across all grade levels. This descriptive study aims to provide a detailed account of the implementation of student agency-driven science practices over a whole school year with an emergent design approach. Qualitative analyses of teacher-researcher co-design meetings, classroom observation notes, and student-created artifacts elaborated the dynamic processes of how student agency-driven science practices were planned, initiated, and reorganized in the classroom over time. Qualitative and content analysis of the teacher’s weekly reflection journals characterized the teacher’s roles in facilitating student-directed science inquiry. These results shed light on an emergent design approach to foster student agency and sustain agency-driven science practices in science classrooms.