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Use client-side file encryption rather than turning on NAS-wide volume encryption. The practical pattern is to create a Cryptomator vault inside a restricted NAS share, unlock it from a trusted computer, and work through its mounted virtual drive. The NAS stores only encrypted vault files; encryption and decryption happen on the client. Lock the vault when finished and back up the encrypted vault data.
This protects selected files without changing how the rest of the NAS is stored. It does not, however, hide every piece of metadata or protect plaintext while the vault is open on a compromised computer.
Why encrypt individual NAS files?
Volume encryption protects an entire storage volume, which is useful when the main concern is a stolen disk or an offline NAS. It is broader than many households and small teams need. You may have a few folders containing tax records, medical documents, contracts, source code, or client material while the rest of the NAS contains ordinary media and shared files.
File or folder encryption narrows the protected area. According to the National Institute of Standards and Technology (NIST), “File encryption is the process of encrypting individual files on a storage medium and permitting access to the encrypted data only after proper authentication is provided.” A client-side vault applies that model before data is written to the NAS. A NAS administrator, backup job, or service that can read the share receives ciphertext rather than the documents’ plaintext.
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The distinction is important. Volume encryption generally protects data at rest on the NAS and is normally controlled by the storage system. A client-side vault keeps the decryption key and plaintext handling on an authorized endpoint. That separation is the reason to choose it when the NAS, its administrator, or a NAS service should not be able to read the sensitive files.
How a client-side NAS vault works
The vault is an encrypted directory
Cryptomator describes itself as “a client-side encryption tool for cloud storage services.” Its security documentation says it encrypts file contents, file and folder names, and obfuscates the directory structure. The same design works with a network share: the share is the vault’s storage location, while the Cryptomator application on your computer presents a decrypted working view.
The NAS does not see a normal folder tree such as Clients/Acme/Contracts. It stores encrypted files and directories generated by the vault. When you unlock the vault, a virtual drive appears on the client. You open and save documents there as if they were on a local drive. Cryptomator’s architecture documentation states: “With every access on your files inside the virtual drive, Cryptomator will en- and decrypt these files on-the-fly.”
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What the NAS and network observe
Network file operations still occur. The NAS can see that a vault share exists, that an authorized account is accessing it, approximate traffic volume, encrypted object sizes, and file-system timestamps. It cannot use those observations to reconstruct the document contents without the vault password and the client-side encryption process.
Anyone who can log in to the NAS with permission to the share can usually delete or damage the ciphertext. Encryption provides confidentiality, not automatic protection from deletion, ransomware, or an administrator with write access. Backups and least-privilege permissions remain necessary.
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Set up a Cryptomator vault on a NAS
NAS interfaces differ by vendor and operating-system version, so the share-creation labels may vary. The sequence below uses generic terms and keeps the security decisions explicit.
- Create a dedicated share. In the NAS administration console, create a new share solely for the encrypted vault. Do not mix ordinary files with vault data unless you have a specific reason. Give the share a name that does not reveal the documents it contains.
- Restrict access. Create or select a NAS user group containing only the people and devices that need the vault. Grant that group read/write access to the dedicated share; remove broad “everyone” or guest permissions. Disable unused accounts and require strong, unique NAS credentials.
- Install Cryptomator on each trusted client. Install the desktop or mobile version appropriate for every computer that will open the files. Each client must be treated as part of the security boundary because it will receive decrypted data while the vault is unlocked.
- Connect the share to the client. Mount the NAS share using the operating system’s normal network-drive or network-volume function. Use a private network or a secure remote-access method rather than exposing the file-sharing protocol directly to the internet.
- Create the vault. In Cryptomator, choose the option to add or create a vault and select the mounted NAS share as its storage location. If you are uncertain about network-share behavior, create a test vault locally first, verify that opening, editing, locking, and reopening work, then copy the complete encrypted vault directory to the dedicated share and add that location in Cryptomator.
- Choose the password carefully. Use a long, unique vault password that is not reused for the NAS account, email, or password manager. Cryptomator cannot recover a forgotten password for you. Store any recovery material or password record in a separate protected location, not in the same share as the vault.
- Unlock and mount. Select the vault in Cryptomator, enter the password, and choose the client’s mount or unlock action. The application creates a virtual drive or mounted location. Confirm that you can create a small test file, close it, lock the vault, unlock it again, and read the file.
- Move sensitive data into the mounted drive. Copy documents into the virtual drive and edit them there. Do not edit the original unencrypted copy and assume the encrypted version is a secure replacement; securely delete unnecessary plaintext originals after verifying the vault copy.
- Close applications before locking. Save and close word processors, image editors, databases, terminals, and sync utilities that have files open in the virtual drive. Open handles can prevent complete locking or leave temporary data behind.
- Lock and unmount. Use Cryptomator’s lock action, then disconnect the network share when it is no longer needed. Check that the virtual drive has disappeared and that no application still displays a plaintext file.
- Back up the encrypted vault. Back up the entire vault directory, including its configuration and encrypted files, using a method that preserves all files and does not alter their names. Test restoring a copy to a separate client before treating the backup as reliable.
What is protected and what remains visible?
Encryption changes the confidentiality of file contents and names, but it does not make the vault invisible. Cryptomator’s documentation identifies several metadata limits.
| Item | Expected protection | Practical implication |
|---|---|---|
| File contents | Encrypted before storage | A reader of the NAS share should see ciphertext rather than document text, provided the client was not compromised. |
| File and folder names | Encrypted or obfuscated by the vault format | Names such as “Payroll” or “Patient-Records” are not stored as ordinary directory names. |
| Directory layout | Obfuscated | The original hierarchy is not presented as a normal NAS folder tree. |
| Access, modification, and creation timestamps | Not fully hidden | An observer may infer when encrypted objects were created or changed. |
| Number of files and folders | Not hidden | Counts can reveal the scale of the collection even when names are concealed. |
| Stored-file sizes | Not hidden | Large or unusually sized encrypted objects can reveal approximate document sizes. |
| Existence of the vault | Not hidden | The share and its encrypted-file patterns can show that a protected collection exists. |
| Plaintext while unlocked | Not protected from a hostile client | Applications and malware on the client can potentially read the mounted files. |
These limits matter when your threat model includes traffic analysis, an administrator who can inspect file metadata, or an endpoint that may already be infected. They are usually acceptable when the primary requirement is to keep document contents and names out of the NAS’s ordinary file view.
The client is a trust boundary
When the vault is locked, the NAS holds encrypted data. When it is unlocked, the client must decrypt files for applications to use them. Cryptomator warns that it cannot protect files on a computer infected with malware that reads passwords or plaintext from an unlocked vault.
Use a supported, patched operating system; keep endpoint protection enabled; and avoid unlocking the vault on shared or unmanaged computers. Lock it before leaving the workstation. Do not paste the vault password into scripts, screenshots, ticket systems, or chat.
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Plaintext can also escape through normal application behavior. Office suites, editors, photo tools, search indexers, crash reporters, and backup programs may create temporary files, autosave copies, thumbnails, or local caches outside the mounted drive. Cryptomator specifically warns that other programs may create backup copies outside the vault. Configure applications to minimize autosave and cache locations, and inspect the client when handling especially sensitive material.
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All three can protect data, but they solve different workflow problems. Choose based on how often the files change, how many clients need access, and whether you need a virtual drive or a single archive.
| Option | Storage model | Best fit | Important trade-offs |
|---|---|---|---|
| Cryptomator vault | File-based encrypted vault presented as a virtual drive | A frequently used set of files and folders on a NAS | Convenient per-file updates and protected names; metadata such as timestamps, counts, and sizes remains partly visible; each client must be trusted. |
| VeraCrypt file-hosted container | One encrypted container mounted as a volume | A collection that can live inside one large container | Provides volume-like behavior, but resizing, concurrent access, and backup handling require planning. A single damaged container can affect many files. |
| 7-Zip encrypted archive | An encrypted archive containing a selected bundle | Occasional transfer, handoff, or cold storage | Simple for a snapshot, but inconvenient for continuously edited files because the archive must be reopened and updated. Extracted files can leave plaintext copies. |
Compare the options on these questions
- File-by-file or one container: File-based storage usually produces smaller, incremental changes; a container treats the collection as one mounted volume.
- Name protection: Confirm whether filenames and directory names are encrypted, not just file contents.
- Metadata leakage: Check what timestamps, sizes, counts, and access patterns remain visible.
- Multiple clients: Decide whether several computers must open the data and how you will prevent simultaneous conflicting writes.
- Backup behavior: Ensure your backup system copies the encrypted data consistently and can restore a complete, usable set.
- Plaintext exposure: Account for editor caches, temporary files, indexing, previews, and local backups on every client.
For active, multi-file work on a NAS, a Cryptomator vault is generally the most natural fit. A VeraCrypt container is reasonable when a single mounted volume is acceptable and you can manage its size and access discipline. Use a 7-Zip archive for an occasional encrypted bundle rather than a working folder.
NAS security controls you still need
Client-side encryption is one layer, not a replacement for NAS administration. Apply the controls recommended in Synology’s security guidance, updated 27 May 2026, regardless of whether you use DSM or another NAS platform.
- Least-privilege permissions: Give the vault share access only to named users and groups that need it. Separate read-only backup identities from accounts that can delete data.
- Account protection: Disable unused accounts, use unique passwords, enable multifactor authentication where the NAS supports it, and configure lockout or rate-limiting controls.
- Updates: Keep the NAS operating system, file-sharing services, and installed packages current. Security fixes do not protect a client-side password, but an unpatched NAS can still expose or destroy the ciphertext.
- HTTPS administration: Use HTTPS for the NAS management interface and web applications. This protects credentials and administrative sessions in transit; it does not turn an ordinary file-sharing connection into end-to-end document encryption.
- Security review: Run the platform’s security advisor or equivalent checks, review public exposure, remove unused services, and monitor authentication logs.
- Network separation: Keep management interfaces off untrusted networks and use a secure remote-access design instead of forwarding NAS file-sharing ports directly to the internet.
Volume encryption may still be worthwhile as a broader at-rest control. It can protect all data if disks or the entire NAS are removed, but it does not provide the same separation from a storage administrator or NAS service that cannot see plaintext in a client-side vault.
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Backups, synchronization, and recovery
Back up ciphertext, not an unlocked drive
Back up the locked vault directory. A backup system that reads the NAS share receives encrypted files and can store them without learning the document contents. If your backup software runs on a client while the vault is unlocked, it may instead copy the mounted plaintext view; choose the source deliberately.
Preserve the complete vault
Do not select a few visible encrypted files manually unless the vault format’s documentation explicitly says that partial copying is safe. Copy the complete vault directory and retain its internal structure. Keep at least one backup independent of the NAS, such as a separately protected storage device or remote repository.
Test a real restore
On a separate, trusted client, install Cryptomator, add the restored vault, and unlock it with the recorded password. Open representative documents and verify that filenames, directory structure, and recent edits are present. A backup that has never passed a restore test is only an assumption.
Handle synchronization carefully
Do not let two clients edit the same vault concurrently unless you understand how your file-sharing and synchronization system handles locking and conflicts. A synchronization tool that creates conflicting copies of encrypted vault files can make recovery harder. Close the vault before copying or synchronizing when practical, and retain versioned backups so an accidental overwrite is reversible.
Troubleshooting common failures
The vault will not lock
Close every application that opened a file from the virtual drive, including background previewers and search tools. Wait for pending saves, stop jobs that are scanning the mounted drive, and disconnect the network share after Cryptomator reports the vault locked. If a process still holds a file, ending that process or restarting the client may be necessary; save work first.
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- Subscription-Free Personal Cloud – Store, back up, and manage all your videos, music, and photos and access them anytime without paying any monthly fees.
- Storage Purpose-Built for Data Security – A NAS designed to keep your data safe, the LS200 features a closed system to reduce vulnerabilities from 3rd party apps and SSL encryption for secure file transfers.
- Back Up Multiple Computers & Devices – NAS Navigator management utility and PC backup software included. NAS Navigator 2 for macOS 15 and earlier. You can set up automated backups of data on your computers.
Files appear corrupted after a network interruption
Do not keep editing while the share is unstable. Reconnect the NAS, verify that the vault directory is complete, and compare it with a known-good backup. Restore to a separate location and test the restored vault before replacing the working copy.
Another client cannot open the vault
Confirm that the second client is using a compatible Cryptomator version, has read/write access to the share, and is pointed at the vault’s root directory rather than a nested encrypted object. Enter the vault password locally; never send it to the NAS administrator or store it in a share.
The backup job reports many changed files
Encrypted vault formats can update several encrypted objects when a document changes. Check whether the backup is copying the locked vault and whether it supports versioning. Do not “optimize” the job by excluding files based on unfamiliar encrypted names; exclusions can make the vault unrecoverable.
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A document still appears in a local search or recent-files list
That is evidence of client-side exposure, not a failure of vault encryption. Remove unnecessary temporary copies, review application cache and autosave settings, and clear recent-file entries according to the operating system and application’s controls. For highly sensitive work, use a dedicated, hardened client.
Quick Recap
A practical decision checklist
- Choose a dedicated NAS share with no guest access.
- Decide which users and which client devices are actually trusted.
- Use a unique vault password and store recovery information separately.
- Validate create, edit, lock, unlock, and restore operations with test data first.
- Keep sensitive files inside the mounted virtual drive, not beside it.
- Close applications and lock the vault whenever work stops.
- Back up the complete locked vault and test recovery on another client.
- Keep NAS accounts, firmware, packages, HTTPS administration, and network exposure under review.
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