Systems and methods are provided for estimating the flow velocity of a multi-phase flow in a pipe using injected microbubbles in combination with ultrasonic signals produced by transducers external to the pipe. The transducers can be located so that one transducer/receiver pair is downstream from a second pair by a separation distance. The receivers can preferably be located in alignment with the transducers for receiving a desirable amount of signal emitted from microbubbles that are excited by absorption of energy from a signal generated by a transducer. The frequency of the signal emitted by the microbubbles can correspond to a harmonic and/or sub-harmonic of the frequency of the signal generated by the transducer. In order to improve the signal-to-noise ratio, frequencies corresponding to a primary frequency emitted by a transducer can be filtered out.