Teaching students to use and interpret different representational tools is critically important if they are to be scientifically literate, to understand how scientific ideas and concepts are represented and to appreciate how scientists think and act. Moreover, students not only need to be competent at using and explaining representations and learning new representations quickly but they also need to have opportunities to work cooperatively with others as it is through interactions between learners, tools and the environment that learning occurs. The current case study (part of a larger study) aimed to: (a) identify the effects of different teacher-introduced representational tools on students' conceptual understandings, dialogic processes, motivation and learning; (b) examine the representational tools used by students during their inquiry science; and (c) examine the physiological states indicative of engagement and cooperation during learning activities. Prior to and on completion of the curriculum unit, participants completed a series of measures to assess actual as well as self-perceived ability in science. Students also wore wireless wristbands to measure autonomic arousal level that were analysed to assess the level of synchrony in physiological states between children. The results showed that the teacher successfully used embodied representations to engage the students in the science unit and maintained their focus in the cooperative groups by using language that encouraged on-going participation in the task. In turn, the students remained on-task and the majority of the language they employed was used to construct and communicate their scientific understanding to others. This high-level common engagement during whole class activities and student-centred learning during the cooperative group activities were also reflected in the physiological measures of synchrony between students. By integrating the video and biometric data with the data from the individual assessments, we construct a rich picture of relationship between the teacher's use of multimodal representations and cooperative small groups with the students' use of scientific language, physiological engagement and their beliefs and attitudes towards science.