During the last decades most of the research in science education has focused on the diagnosis and documentation of students' difficulties in understanding sciences. These investigations have shown that students have frequent misperceptions of basic dynamics which in addition to appear across situations and domains, are strongly resistant to traditional education. We propose an analytical framework to interpret the cognitive effects of system dynamics interventions in students' science knowledge. Based on a cognitive theory of science learning denominated coordination, we suggest 'seeing in levels' -thought as the ability to recognize the stock and flow structure of a system- as an appropriate mechanism for addressing students misconceptions of dynamics in school sciences. We argue that 'seeing in levels' may help students in reasoning about scientific concepts, given that it provides a strategy for both thinking and organizing perception.