The present study examines the interconnectedness of spontaneous scientific argumentation and socially shared metacognitive regulation (SSMR) during a collaborative inquiry in which students are tasked with working in a virtual learning environment for marine biological issues. From a larger dataset of 39 groups, four small student groups were selected for this specific study. Of the selected groups, two were high-performing and two were low-performing based on their collaborative outcomes. Moreover, students' videotaped discussions were analyzed in terms of argumentation and metacognitive regulation during three phases (planning, experimenting, and presenting). Finally, an in-depth video analysis was conducted, which was supported by qualitative excerpts that were transcribed. The results of the present study demonstrate that metacognitive regulation and argumentation spontaneously co-occur; in particular, SSMR appeared to co-occur with high-level argumentation. Moreover, SSMR was shown to be related to deeper argumentation and, thus, to the discussion of the high-performing group. Finally, the results hinted that students socially regulate their learning when they are asking questions related to a scientific topic, even though this was not shown to be statistically significant. To summarize, the interrelation of scientific argumentation and metacognitive regulation is under-researched and, therefore, the present study attempts to extend the understanding of this relationship and the co-occurrence of argumentation and metacognitive regulation.