Systems and methods for estimating frequency drifts in magnetic resonance signals acquired with a magnetic resonance imaging (“MRI”) system are provided. In one example, the frequency drifts are estimated from phase-correction data that are obtained during an echo-planar imaging (“EPI”), or other multiecho imaging, scan. The systems and methods of the present invention provide for efficiently and accurately computing frequency drift values that can be used for real-time, prospective frequency drift correction.