Provided are a method, system, and program for managing data in storage units. Storage pool information indicates an assignment of a plurality of storage units to a plurality of storage pools, wherein each pool is assigned zero or more storage units, wherein data associated with one storage pool is stored in a storage unit assigned to the storage pool, wherein the storage pool information for each pool indicates a threshold and target storage pool, and wherein the target storage pool is capable of being different from the storage pool. One storage unit associated with a source storage pool is selected and a determination is made of the threshold from the storage pool information for the source storage pool. A determination is made of whether the selected storage unit satisfies the determined threshold and if the selected storage unit satisfies the determined threshold, then a target storage unit in the target storage pool is selected if the storage pool information for the source storage pool indicates a target storage pool different from the source storage pool. Data from the selected storage unit is copied to the selected target storage unit.