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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.