Most NAS units have two or three USB ports that end up holding a single backup drive for years and doing nothing else. That’s a lot of unused capacity, especially now that USB 3.2 Gen 2 (10 Gbps) is standard on the mid-range boxes from Synology, QNAP, and UGREEN. Turning those ports into a proper part of your storage plan, external staging, versioned backups, sneakernet for large transfers, needs the right desktop app on the other end. We tested seven of the best for real workflows across Synology DSM, QNAP QTS, and TrueNAS.
What to look for in a NAS USB workflow app
- Bidirectional sync, not just backup. A backup runs one way. A sync keeps both sides mirrored, which is often what you actually want.
- Deduplication and versioning. Modern backup tools store diffs, not full copies. That’s how a 100GB source fits into 30GB over a year.
- Encryption at rest. Data on a USB drive walks out the door easily. Full-drive or per-file encryption matters.
- Cross-platform. Windows and macOS and Linux clients matter if you have more than one machine talking to the same USB drive.
- CLI vs GUI. Some are made for scripts and cron. Some want a window and a button.
Quick comparison
| App | Best for | Platforms | Price |
|---|---|---|---|
| Syncthing | Continuous bidirectional sync | Windows, macOS, Linux | Free, open source |
| rclone | Scriptable multi-cloud sync | Windows, macOS, Linux | Free, open source |
| Duplicati | GUI backup with versioning | Windows, macOS, Linux | Free, open source |
| Kopia | Modern deduplicated backup | Windows, macOS, Linux | Free, open source |
| Restic | CLI-first backup, wide support | Windows, macOS, Linux | Free, open source |
| FreeFileSync | Simple two-way sync | Windows, macOS, Linux | Free / donation |
| Veeam Agent | Full-system Windows backup | Windows, Linux | Free (Agent) |
1. Syncthing — Best continuous sync
Syncthing is a peer-to-peer sync tool that keeps folders identical across devices. Point one end at a folder on your desktop, the other end at a USB drive mounted on your NAS. Any change on either side propagates. No cloud in between.
For NAS USB workflows this is the best fit when you want the USB drive to be an always-current mirror of a working directory (photos, video edits, project archives) that you also want available on the NAS side.
Where it falls short: it’s a sync tool, not a backup tool. If you delete a file, it deletes on both ends. Enable versioning on the receiving side.
Download: Syncthing
Bottom line: best pick when the USB drive is a working mirror.
2. rclone — Best scriptable transfer
rclone is the CLI Swiss army knife for storage. It talks to 40-plus backends (SFTP, S3, WebDAV, and every major cloud), which matters when the NAS presents its USB drive as an SFTP share and you want a script-driven sync.
Encrypt on the fly with the crypt backend. Add rate limiting. Chain it into cron.
Where it falls short: it’s a command line tool. The learning curve is real.
Download: rclone
Bottom line: the tool for scripted, scheduled, encrypted transfers.
3. Duplicati — Best GUI backup with versioning
Duplicati is what you install when you want a proper backup workflow (compressed, encrypted, versioned) with a web UI you can bookmark. Point it at a NAS SFTP share that reads from the USB drive and it handles the rest.
Retention policies (keep daily for 7 days, weekly for a month, monthly for a year) are configurable from the UI.
Where it falls short: restore performance from very large archives can be slow.
Download: Duplicati
Bottom line: the friendliest GUI backup that still does versioning right.
4. Kopia — Best modern deduplicated backup
Kopia is Duplicati’s newer competitor. It writes content-addressable, deduplicated repositories that grow far slower than traditional incremental backups. Cross-platform GUI plus a CLI, native support for SFTP, WebDAV, S3, and mounted-filesystem targets.
Restoration speed is a real advantage over Duplicati on our large test set.
Download: Kopia
Bottom line: the newer, faster answer to Duplicati.
5. Restic — Best CLI-first backup
Restic is the CLI-first alternative that a lot of self-hosters run. Deduplication, encryption, and a clean repository format. Wide backend support including SFTP for NAS USB drives.
Pair with Backrest or Autorestic for scheduling if you’d rather not write your own cron.
Download: Restic
Bottom line: the CLI backup the sysadmin crowd trusts.
6. FreeFileSync — Best simple two-way sync
FreeFileSync does one thing and does it well: compare two folders, sync them, show you a diff before it commits. If the NAS mounts its USB drive as a SMB share and you want a manual “sync this now” workflow, FreeFileSync is the calm option.
Download: FreeFileSync
Bottom line: the tool for the person who wants to see what will change before it changes.
7. Veeam Agent — Best full-system Windows backup
Veeam Agent for Microsoft Windows does image-level backup of a whole Windows machine. Point it at an SFTP share on the NAS reading from the USB drive and you have a real system-restore path.
Download: Veeam Agent
Bottom line: the pick when you need a full-system Windows recovery target.
How to pick
- You want a working mirror. Syncthing.
- You need scripted transfers. rclone.
- You want a GUI backup with versions. Duplicati or Kopia.
- You’d rather run a command. Restic.
- You want to see the diff before you sync. FreeFileSync.
- You need a full Windows image restore. Veeam Agent.
FAQ
Should I use the NAS USB port for backup or for extra storage?
Either works, but the two roles are different. As backup, treat the USB drive as an offline copy of NAS data (rotate at least two drives). As extra storage, expose it as an SMB share and back it up separately to a different target.
Are USB 3.2 Gen 2 speeds actually usable for backup?
Yes. 10 Gbps line rate translates to around 1000-1050 MB/s in practice with a good drive. That’s faster than any spinning disk and comparable to a mid-range NVMe.
Can I encrypt a USB drive attached to a NAS?
Yes, at either end. Format the drive as LUKS on Linux (or use encrypted-share features in Synology’s Hyper Backup, QNAP’s Hybrid Backup Sync, or TrueNAS’s ZFS encryption). Kopia, Restic, and Duplicati also encrypt at the backup layer regardless of the underlying volume.
