A method and system are disclosed for estimating origin and destination locations of users of a transportation system. The origins and destinations of known users are determined during a segment of an analysis period from validation information for all users of the transportation system. The origins and destinations are then mapped to probable locations associated with the transportation network. A destination probability is then computed for each destination location of an individual origin location. A unknown users are then apportioned to each destination, which may be based on the number of unknown users on a vehicle traveling from the origin to the destination, the computed probability, and the validation information, so as to estimate the number of users traveling from an origin location to any corresponding destination location on the transportation system.