A method and system are disclosed for dynamically estimating an origin-destination matrix. An origin-destination matrix is initialized with a set of origin stops and destination stops. Validation sequences are acquired for a set of travelers on a transportation system which include a plurality of the origin stops and respective timestamps. Corresponding destination stops may be known or inferred. For each validation sequence, a set of subsequences is generated, each including a respective one of the origin stops and the associated timestamp. Subsequences which, in combination, constitute a valid transfer trip are identified. For a combination of subsequences constituting a valid transfer trip, the method includes determining whether the valid transfer trip is a multi-goal trip for which there is least a first destination stop with an intermediate goal and a second destination stop with a final goal. The origin-destination matrix is updated, based on the determination.