A video transmitter identifies regions in pictures in a compressed three-dimensional (3D) video comprising a base view video and an enhancement view video. The identified regions are not referenced by other pictures in the compressed 3D video. The identified regions are watermarked. Pictures such as a high layer picture in the base view video and the enhancement view video are identified for watermarking. The identified regions in the base view and/or enhancement view videos are watermarked and multiplexed into a transport stream for transmission. An intended video receiver extracts the base view video, the enhancement view video and corresponding watermark data from the received transport stream. The corresponding extracted watermark data are synchronized with the extracted base view video and the extracted enhancement view video, respectively, for watermark insertion. The resulting base view and enhancement view videos are decoded into a left view video and a right view video, respectively.