A learning path has been developed on system dynamical graphical modelling, integrated into the Dutch lower secondary physics curriculum. As part of the developmental research for this learning path, students' understanding of the relation structures shown in the diagrams of graphical system dynamics based models has been investigated. One of our main findings is that only some students understand these structures correctly. Reality-based interpretation of the diagrams can conceal an incorrect understanding of diagram structures. As a result, students seemingly have no problems interpreting the diagrams until they are asked to construct a graphical model. Misconceptions have been identified that are the consequence of the fact that the equations are not clearly communicated by the diagrams or because the icons used in the diagrams mislead novice modellers. Suggestions are made for improvements.