The assessment of station designs by applying pedestrian flow simulation models is addressed. In particular, station design issues pertain to the way access gates will affect pedestrian flow operations in regard to levels of service, congestion levels, average walking times, delays incurred at gates, and so forth. Effects of different system layouts are studied, as well as the difference between different gate systems (low- and high-capacity systems), in regard to processing passenger flows. Finally, pedestrian flow operations in case of emergency situations are of interest. To examine those issues, pedestrian traffic operations for different station design alternatives are predicted with the dynamic microscopic pedestrian flow model NOMAD. That is done for reference situations (validation) as well as for design alternatives. The NOMAD model has been extended with a new module describing pedestrian operations (i.e., user-optimal gate choice) at the gates. It is found that the simple design guidelines used to set up the design alternatives provide a satisfactory level of service to transferring pedestrians and that the gates can be installed without compromising passenger safety. Nevertheless, the need to reroute, inefficient gate use, and interactions between conflicting pedestrian flows cause small but significant delays to transferring pedestrians that cannot have been predicted without the use of an adequate microsimulation model.