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This study examined affect during high school students' face‐to‐face collaborative inquiry learning in science, supported by the web‐based software Virtual Baltic Sea Explorer. Self‐reported affective states during the inquiry process in peer groups were related to evaluations of a group's collaboration and performance in three phases of interdisciplinary science inquiry (biology and chemistry). Results indicate that despite high cognitive demands, positive affect prevailed whereas negative affect was infrequent. Structural equation modelling was used to analyse the significance of affect on collaboration and group performance. The relationship between affect, collaboration, and the groups' productive outcome revealed that self‐assurance had a significant effect on collaboration and support, intertwined with scientific understanding and group performance. Furthermore, a cross‐lagged analysis showed a reciprocal relation between positive affect, scientific understanding, collaboration, and support. These outcomes contribute to the scarce literature on the nature and importance of affect in the process of face‐to‐face computer‐supported collaborative inquiry and learning in science. Lay Description: What is already known about this topic: Positive collaboration in groups promotes positive affect.Positive affect is crucial for attitudes and motivation towards science learning.Affect is an important factor in virtual learning environment design, but there is a lack of understanding on occurrence and influence of affect during face‐to‐face virtual learning.What this paper adds: Students report mainly positive affect during virtual science inquiry despite tough task demands and the level of productive group outcome.Positive activating affect prevails throughout collaborative inquiry, whereas negative deactivating affect is subordinate.Joviality and notably self‐assurance has a great impact on collaboration and support, and achievement, whereas feelings of displeasure and insecurity may have negative implications.Implications for practice and/or policy: Self‐assurance promotes collaboration and support and the aim at coconstruction of shared understanding during virtual science inquiry learning.Efforts should be made to enhance positive affect and especially self‐assurance in virtual learning. [ABSTRACT FROM AUTHOR]