A method of segmenting a media signal for parallel watermarking operations sub-divides the media signal into segments, distributes the segments to parallel processors, and performs parallel digital watermark operations on the segments in the parallel processors. These parallel processors may comprise separate threads of execution on a processing unit, or several execution threads distributed to several processing units. In one enhancement, the method prioritizes the segments for watermarking operations. This enables finite processing resources to be allocated to segments in order of their priority. Further, processing resources are devoted to segments where the digital watermark is more likely to be imperceptible and/or readable. A system for distributed watermark embedding operations includes a watermark signal generator, a perceptual analyzer and a watermark applicator. The system supports operation-level parallelism in the concurrent operation of watermark embedder modules, and data parallelism in the concurrent operation of these modules on segments of a media signal to be embedded with an imperceptible digital watermark.