A system and method is provided for acquiring flow encoded data from a subject using a magnetic resonance imaging (MRI) system. The method includes acquiring flow encoded (FE) data with alternating encoding polarities and along two of three orthogonal directions through the subject over at least two cycles of the flow within the subject； and separating the FE data into directional FE datasets using a temporal filter that separates the FE data based on temporal modulation of the FE directions caused by the alternating encoding polarities extending over the at least two cycles of the flow within the subject that shift the Fourier spectrum of velocity waveforms corresponding to the FE data. The method also includes using the directional FE datasets to generate an image of the subject showing flow within the subject caused by the at least two cycles of flow within the subject.
