A central aspect of learning chemistry is learning to relate observations of phenomena to models of the sub-microscopic level of matter, and hence being able to explain the observable phenomena. However, research shows that students have difficulties discerning and comprehending the meaning of the sub-micro level and its models, and that practical work in its traditional form fails to help students to discern the relation between observations and models. Consequently, there is a strong call for new teaching activities to address these issues. This paper emerges from a growing number of studies showing that learning is supported when students are set to cooperatively create their own multimodal representations of science phenomena. In this paper, we explore the approach of letting students create their own stop-motion animation as a means to explain observations during practical work. The students’ work of producing a phenomenon in the laboratory and creating an animation was recorded (audio–video) to capture students’ verbal and non-verbal interactions and use of resources. Data was analysed using a thematic content analysis with a deductive approach aimed at identifying the aspects of chemistry content that are being reasoned. The analysis showed that the task enabled students to engage in reasoning concerning both the observations and the sub-micro-level models, and how they relate to each other. The task also enabled students to reason about features of the representation that are needed to make sense of both the observational and sub-microscopic aspects of a phenomenon, as well as reflecting upon the meaning of a model.