Contemporary teaching and learning approaches expect students--at any level of education--to be active producers of knowledge. This leads to the need for creation of instructional strategies, learning environments and tasks that can offer students opportunities for active learning. Research argues that one of the most meaningful and engaging forms of active learning is modelling, that is using computational environments to build representational and epistemological models of the phenomena that are being studied, following the essential features of inquiry based science and mathematics education. The aim of the article is to investigate the impact of the computational experiment approach on: a) students' learning performance, b) the use of modelling indicators c) the motives and d) the scientific epistemic beliefs. K-12 students in a Greek school participated in the experiment and the methodology of the computational experiment was implemented using three software tools, namely: the Modellus software, the Interactive Physics (IP) software and the Easy Java Simulator Software (EJS), in order to study the concept of the simple harmonic motion (equations of motion, dynamics and energy consideration). All applications were developed using the essential features of inquiry based science education in the framework of the computational approach methodology and the model was considered as the fundamental instruction unit. The findings suggest that the inquiry based computational experiment using Easy Java Simulator(EJS) is more effective in enhancing the conceptual understanding of students as well as the use of modelling indicators, and these results may have implications for the effectiveness of the computational experiment methodology when it is combined with the EJS Tools.