A system and method for motion-based adaptive frequency estimation of a Doppler sensor is provided. The system comprises a Doppler sensor configured to output a digitized Doppler data signal, and a Doppler velocity estimation module operatively coupled to the Doppler sensor to receive the Doppler data signal. An inertial navigation system is operatively coupled to the Doppler velocity estimation module, and one or more inertial sensors is operatively coupled to the inertial navigation system. The inertial sensors are configured to transmit inertial navigation data to the inertial navigation system. The Doppler velocity estimation module calculates a speed or velocity estimate based on the Doppler data signal and the inertial navigation data. The speed or velocity estimate is then transmitted to the inertial navigation system.