Provided are a method, system, and program for maintaining an aggregate including active files in a storage pool. One active-only storage pool is included in a plurality of storage pools. Each storage pool includes files and the active-only storage pool is intended to include only active files and not inactive versions of files. The active-only storage pool includes at least a first aggregate including a plurality of files. One file is deactivated in the first aggregate in the active only storage pool to produce an inactive version of the file, wherein the first aggregate includes the inactive version of the file. A determination is made of inactive versions of files in the first aggregate. A second aggregate is generated in the active only storage pool including the active files from the first aggregate and not including the determined inactive versions of files from the first aggregate. The second aggregate replaces the first aggregate in the active-only storage pool.