With a sizeable expected growth of demand for rail transport in the Netherlands in the coming decades, and limited resources for expansion of the rail network, intensified utilization of the infrastructure is to be expected. To adequately manage this growth, appropriate tools for policy analysis are needed. The possibilities and pitfalls of using System Dynamics for policy analysis in the Dutch rail system have been explored by performing a modelling study into the interrelations of modal split, mobility and operations using System Dynamics. Additional scrutiny is placed on the method, because of the unstructuredness of many problems in the rail sector, and decision-making in a network type environment. Results show that the reliability of infrastructure is a major component in the extent of delays. Furthermore, the effect of unreliability in a train trip and the characteristics of a car trip are important for the choice between train and car. Although classical policy analysis has proven to be possible, modelling the operational part of the system has proven challenging due to the spatial and discrete characteristics of parts of the system. Recommendations are given to improve the model and model use to better suit the unstructuredness of the problems.