A computer-implemented method for managing references in deduplicating data systems may include (1) identifying a first instance of a data segment stored within a deduplicating data system that reduces redundant data storage by storing at least two data objects such that each of the two data objects references the first instance of the data segment, (2) identifying an additional data object to be stored by the deduplicating data system that includes the data segment, (3) determining whether a reference limit associated with the first instance of the data segment has been reached, and (4) storing, based at least in part on determining that the reference limit associated with the first instance of the data segment has been reached, a second instance of the data segment within the deduplicating data system. Various other methods, systems, and computer-readable media are also disclosed.