A method for the measurement of the flow rate in a pipe system is proposed. The method utilizes the vibration signals measured by three accelerometers which are mounted on the surface of the pipe. The main advantage of the proposed method is that it does not require any sensory system inside of the piping system, therefore it does not disturb any characteristics of the flow. To measure the flow rate, the change of the wavenumber which is one of the results caused by the flow rate change is estimated by applying the wave decomposition theory. The wavenumber change of the wave propagating along a pipe can be modeled to be proportional to the flow rate at the low frequency range. The wave decomposition theory is used to estimate the wavenumber change by measuring the vibration signals at discrete three positions, which requires the measurement system being composed by three sensors; in this study three accelerometers are used. All possible errors associated with the proposed measurement system are theoretically as well as experimentally investigated. Those are errors due to noise, sensor spacing, sensor position with respect to boundaries, and finally phase as well as magnitude mismatch between sensors. Numerical simulations and experiments on the steel and aluminum pipes with water flow show the potential of the proposed measurement method.