Techniques are provided for implementing intelligent defragmentation in a storage system. A storage control system manages a logical address space of a storage volume. The logical address space is partitioned into a plurality of extents, wherein each extent comprises a contiguous block of logical addresses of the logical address space. The storage control system monitors input/output (I/O) operations for logical addresses associated with the extents, and estimates fragmentation levels of the extents based on metadata associated with the monitored I/O operations. The storage control system identifies one or more extents as candidates for defragmentation based at least on the estimated fragmentation levels of the extents.