A computer-implemented method for removing unreferenced data segments from deduplicated data systems may include: 1) identifying a deduplicated data system that contains a plurality of data objects, 2) dividing the data objects within the deduplicated data system into a plurality of data object groups, 3) identifying, within the data object groups, at least one data object group that has changed subsequent to a prior garbage-collection operation that removed data segments that were not referenced by data objects within the deduplicated data system, 4) identifying at least one container within the deduplicated data system that contains data segments referenced by data objects within the changed data object group, and then, for each identified container, 5) removing data segments from the identified container that are not referenced by data objects within the deduplicated data system. Various other methods, systems, and computer-readable media are also disclosed.