Optical Doppler tomography is a valuable functional extension of optical coherence tomography (OCT) that can be used to study subsurface blood flows of biological tissues. We propose a novel frequency estimation technique that uses an adaptive notch filter (ANF) to track the depth-resolved Doppler frequency. This new technique is a minimal-parameter filter and works in the time domain without the need of Fourier transformation. Therefore, the algorithm has a computationally efficient structure that may be well suited for implementation in real-time ODT systems. Our simulations and imaging results also demonstrate that this filter has good performance in terms of noise robustness and estimation accuracy compared with existing estimation algorithms.