The present invention provides systems and methods for loading and unloading substrate carriers onto and off of a transport system. The invention includes a substrate carrier handler adapted to transfer a substrate earner between a docking station and a transport system/ the substrate carrier handler including an end effector adapted to support the substrate carrier; a controller coupled to the substrate carrier handler and operative to control the substrate carrier handler such that the end effector of the substrate carrier handler is operative to selectively engage and disengage the substrate carrier to and from the transport system while the substrate carrier is in motion; and a sensor coupled to the controller and operative to provide a signal to the controller indicative of information about the substrate carrier.