A method of synchronizing a digital watermark detector divides a watermarked signal into blocks, each block including a portion of a watermark signal. For each block, the method computes a local correlation space comprising a neighborhood of correlation values by correlating the watermarked data in the block with a known watermark signal at a neighborhood around the block. It then finds a correlation maxima in the local correlation space for each block, where the correlation maxima indicates a local offset used to align the watermarked data in the block before decoding a watermark message from the block. To further refine the synchronization, the method filters the array of local offsets for the blocks to provide a refined set of offsets. The offsets and corresponding correlation values provide an indicator of where message symbol decoding will provide more accurate results, enabling the watermark message decoder to selectively decode symbols from portions of a signal block containing a watermark signal.