Systems for deduplicating one or more storage units of a storage system provide a scheduler, which is operable to select at least one storage unit (e.g. a storage volume) for deduplication and perform a deduplication process, which removes duplicate data blocks from the selected storage volume. The systems are operable to determine the state of one or more storage units and manage deduplication requests in part based state information. The system is further operable to manage user generated requests and manage deduplication requests in part based on user input information. The system may include a rules engine which prioritizes system operations including determining an order in which to perform state-gathering information and determining an order in which to perform deduplication. The system is further operable to determine the order in which storage units are processed.