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With large volume of passengers boarding and alighting through subway platforms, the stations are getting crowded, resulting in drops in the level of service and safety concerns, especially for subway systems operating at capacity during peak hours. Thus, it is crucial for subway agencies to sense changes in travel demand and adjust their management schemes accordingly. In this paper we propose a statistical approach to estimate dynamic passenger flows with automated data. First, we develop a dynamic logistic model for calculating passenger tap-out times, which can be employed to infer passenger flow characteristics at the aggregate level. In addition, a new passenger-to-train assignment model for any subway route is derived based on the dynamic model. Subsequently, we apply an expectation-maximization algorithm to estimate the model parameters with automated fare collection and automated vehicle location data. Finally, a cross-validation method is employed to validate our approach with data obtained from several routes in Beijing subway system in China. Results of 95% prediction intervals indicate the effectiveness of the models and the proposed estimation methods. • Propose a dynamic logistic model for inferring and predicting subway passenger tap-out times. • Apply an expectation-maximization algorithm for model parameters estimation. • Develop a novel passenger-to-train assignment strategy. • No prior distributions of parameters or additional information required in the proposed methods. • Results show good effectiveness of the models and acceptable accuracy of the prediction methods. [ABSTRACT FROM AUTHOR]