The aim of the present study was twofold. First, we aimed to replicate the findings of previous studies which had showed a substantial improvement on procedural and epistemological knowledge after direct instruction and their maintenance in time. Second, we aimed to examine the dynamic relationships of the procedural (control of variables strategy) and epistemological (nature of models) knowledge and the conceptual understanding of interrelated phenomena (floating-sinking) and subordinate abstract concepts (density) that have been developed to explain these phenomena across the learning process. A five-unit teaching learning sequence was organized and implemented in three 5th grade (N = 53) science classes. Participants answered at three time points--before, immediately following and 7 months after the implementation--in a questionnaire involving eight questions concerning the four above-mentioned teaching and learning content areas. The collected data was used to test, with Path analysis, the validity of the theoretically designed model that depicted the causal relationships between the four areas. The inquiry-based activities were successful in bringing students' ideas closer to the scientific knowledge. In addition, the model fitted in well with our data. So, the instruction of procedural and epistemological knowledge was crucial in the conceptual understanding of density in the frame of floating-sinking interpretation. In addition, understanding of the concept of density as a property of materials immediately following the implementation contributes significantly to students' interpretations of floating-sinking phenomena even 7 months later.