Computational experiment approach considers models as the fundamental instructional units of Inquiry Based Science and Mathematics Education (IBSE) and STEM Education, where the model take the place of the "classical" experimental set-up and simulation replaces the experiment. Argumentation in IBSE and STEM education is related to the engagement of students/learners in a process where they make claims and use models and data to support their conjectures and justify or disprove their ideas. Threshold Concepts (TCs) are of particular interest to IBSE and STEM education, representing a "transformed way of understanding, or interpreting or viewing something without which the learner cannot progress." The purpose of this study is to explore the effects of IBSE teaching approach on University students': (a) argumentation; (b) involvement in the use of modelling indicators; and (c) acquisition of certain threshold concepts in Physics and Mathematics. 79 pre-service engineering school university students participated in this research and results indicate that the computational experiment can help students' acquisition of threshold concepts and improve their level of argumentation as well as the use of modelling indicators.