During collaborative learning, affect is constantly present in groups' interactions, influencing and shaping the learning process. The aim of this study was to understand what type of learning situations trigger affective states in collaborative groups, and how these affective states are related to group members' physiological activation. The participants were 12-year-old primary school students (N = 31, 10 groups) performing a collaborative science task. In the analysis, video data observations were combined with data of group members' physiological activation. The groups' situational valence was identified based on the group members' observed emotional expressions and their physiological activation levels were measured with electrodermal activity (EDA). Results revealed that situations with group members' simultaneous physiological activation were rare compared with the observable emotional expressions. However, when group members indicated physiological activation simultaneously, they also showed visible emotional expressions more often than in deactivating situations. Moreover, the results showed that socially-related factors were more likely to trigger physiological activation with a mixed group level valence. In turn, task-related factors were more likely to trigger physiological activation with a neutral group level valence. The results of this study imply that by combining different process data modalities revealing the different components of affect, it might be possible to track emotionally meaningful situations that shape the course of the collaborative learning process.