Systems and methods for encoding multiple video streams with digital watermarking for adaptive bitrate streaming in accordance with embodiments of the invention are disclosed. In one embodiment, a method for preprocessing multimedia content into streams with watermark information includes receiving a source content media stream, generating at least two variant preprocessed streams for each received source content media stream, where each variant preprocessed stream includes different watermark information in the same locations as the other variant preprocessed streams and where marked locations are spaced apart at least a distance equal to a predetermined maximum segment size, generating a set of embed location information describing marked locations in the variant preprocessed streams, generating at least one variant output stream from each variant preprocessed stream using video compression, partitioning each variant output stream into a set of segments, where each segment is no longer than the predetermined maximum segment size and contains at most one copy of the watermark information, generating a set of segment boundary information describing the boundaries of segments within the variant output streams and the boundaries are the same between variant output streams, and generating a segment selection list using the set of embed location information and the set of segment boundary information, where the segment selection list includes only one variant segment for each segment according to a watermark sequence and the digits of the watermark sequence correspond to the watermark information applied to each variant preprocessed stream.