To estimate urban network travel time, the classical analytical procedure uses cumulative counts at upstream and downstream locations of links. This procedure is vulnerable in urban networks mainly due to significant flow to and from mid-link sinks and sources. Moreover, most urban network links are only equipped with detectors at their end. Therefore without information on the percentage of turning movement at crossroads, the classical analytical procedure is not applicable. The algorithm proposed and validated in this research estimates urban links travel times based on an unscented Kalman filter (UKF). This algorithm integrates stochastically the vehicle count data from underground loop detectors at the end of every link and the travel times from probe vehicles. The proposed methodology can be used for estimating travel time in real-time. Moreover, with this methodology the number of upstream vehicles as well as the number of mid-link sink/source vehicles is estimated for each link.