The present invention relates to a method and system for measuring fluid velocity in pipes alternately transmitting two or more ultrasonic frequencies through a pipe wall into a fluid containing scatterers. For each transmission frequency, energy reflected from the scatterers is mixed with the transmission frequency and the result sampled at a rate which is a constant fraction of the transmission frequency. The combination of the Doppler effect on frequencies reflected from the moving scatterers, and the described sampling rate scheme combine to permit isolation of velocity related frequencies from extraneous frequencies in the reflected energy in a computationally efficient manner. A single frequency which represents fluid velocity is extracted from the gathered data, and the fluid velocity readily calculated therefrom using the Doppler formula. The invention provides a system and method for measuring fluid velocity which is simple, reliable, and cost effective.