Provided are a method, system, and program for maintaining active-only storage pools. A first storage pool includes at least a first aggregate including a plurality of active and inactive files. A second aggregate is generated in a second storage pool. A determination is made of active versions of files in the first aggregate that satisfy at least one criterion. The determined active versions of files are copied from the first aggregate to the second aggregate in the second storage pool, wherein the second aggregate does not include inactive versions of files in the first storage pool.