This study aims at examining the role of metacognition, which refers to one's ability to control and regulate their own thinking process through various activities in assessing dynamics of stocks and flows. The first research question focuses on the metacognitive activities used by individuals who solved such tasks correctly and who did not. The second question focuses on how successfully participants organized their thinking processes to arrive at a correct answer when prompted and permitted to retry. Forty undergraduate students were involved in the study, and concurrent think-aloud protocol was used to examine their thinking when performing two stock-flow tasks. The findings revealed that participants tend to have difficulties in reading, planning, monitoring, and checking activities. The effectiveness of metacognitive activities employed by the participants is likely to decrease from reading to checking, respectively. The study contributes to our understanding of metacognitive deficiencies in stock-flow failure and provides further research suggestions. © 2021 The Authors. System Dynamics Review published by John Wiley & Sons Ltd on behalf of System Dynamics Society.