This study presents a robust model for estimating the dynamic freeway origin-destination matrix with a measurable time series of ramp and mainline flows. The proposed model captures the speed variance among vehicles having the same departure time, origin, and destination with an embedded travel time distribution function that results in a substantial reduction in model parameters. With the developed solution algorithm, the proposed model offers the potential use in a network of realistic size such as the I-95 freeway corridor between the Maryland I-695 and I-495 beltways. Extensive numerical analyses with respect to the sensitivity of both input measurement errors and the selection of initial parameters have revealed that the proposed model is sufficiently robust for real-world applications.