A system and method for adaptive estimation and compensation of clock drift in echo cancellers is provided. The invention includes an acoustic echo cancellation system with a built in adaptive clock drift compensation system. The acoustic echo cancellation system has an AEC component that performs acoustic echo cancellation on data from a capture buffer, by also using information derived from a render buffer. The clock drift compensation system has access to this capture buffer and render buffer. The clock drift compensation system includes a clock drift compensator that calculates, based on the current location of the capture data being processed by the AEC component as well as additional information, the ideal location in the render buffer from which the AEC component should process data. The clock drift compensator further adjusts the current location in the render buffer from which the AEC component processes data based, at least in part, upon this ideal location. The clock drift compensator can further detect and correct for glitches in the hardware positions received from the render and capture devices.