System behaviour usually is modelled with logical operators and triggering conditions on control flows between processes, activities, tasks, or events. This allows branching control flows in order to increase model comprehensibility. In case of Topological Functioning Model (TFM), where system’s functionality is represented by causal relations among functional characteristics, combinations of causes as well as triggered effects may be quite complex. Therefore, specification of them must not decrease apprehensibility of the TFM, while keeping its accuracy, compactness and level of abstraction. Additionally, this specification must also be modifiable and transformable. In this paper we discuss and refine a concept of a cause-and-effect relation and a logical relation in the TFM. Then, we analyze specification means used in BPMN, UML Activity Diagrams, EPCs, flowcharts, Petri Nets and Decision Models and assess which of them are more appropriate for using or integrating with the TFM. The more suitable means will increase the accuracy of specification of logical relations and system behaviour in the TFM. As a result, it would be possible to eliminate human participation in transformations from the TFM to models at the lower level of abstraction.