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 carrier 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. The controller is operative to adjust operation of the substrate carrier handler based on the signal from the sensor if the adjustment may be performed within a load or unload stroke of the substrate carrier handler. Numerous other aspects are provided.