Real-time public transit ridership flow and origin-destination (O-D) information is essential for improving transit service quality and optimizing transit networks in smart cities. The effectiveness and accuracy of the traditional survey-based methods and smart card data-driven methods for O-D information inference have multiple disadvantages in terms of biased results, high latency, insufficient sample size, and the high cost of time and energy. By considering the ubiquity of smart mobile devices in the world, monitoring public transit ridership flow can be accomplished by passively sensing Wi-Fi and Bluetooth (BT) mobile devices of passengers. This study proposed a system for monitoring real-time public transit passenger ridership flow and O-D information based on customized Wi-Fi and BT sensing device. By combining the consideration of the assumed overlapping feature spaces of passenger and nonpassenger media access control address data, a three-step data-driven algorithm framework for estimating transit ridership flow and O-D information is proposed. The observed ridership flow is used as the ground truth for evaluating the performance of the proposed algorithm. According to the evaluation results, the proposed algorithm outperformed all selected baseline models and the existing filtering methods. The findings of this study can help to provide real time and precise transit ridership flow and O-D information for supporting transit vehicle management and the quality of service enhancement.