How to Free Up Space on a Synology NAS by Removing Duplicate Files

To free up space on a Synology NAS, find the duplicate files, keep one copy of each, remove the rest, and then clear the Recycle Bin and old snapshots that still hold the deleted data. You can find duplicates with Synology's Storage Analyzer, by hand in File Station, over SSH, or with a dedicated Synology duplicate file finder such as DT Synology Duplicate File Finder.

If your storage bar has turned red and you cannot say what is filling it, this guide is for you. We will go through why duplicates build up, four ways to find them, how to delete them without losing anything you need, and the one step most people miss: getting the space back after deleting.

Why a Synology NAS Fills Up With Duplicate Files

A NAS is built to keep everything in one place, so it also collects every mistake in one place. Nobody plans to store the same file three times. It happens one small decision at a time.

Phone backups overlap. Photos get backed up from the phone and also imported from a camera card or a laptop. Same picture, two folders.
Folders get copied just in case. Someone copies a project folder before a big edit and never deletes the copy.
Teams save their own versions. Two people download the same spreadsheet from a shared folder and save it again under their own names.
Old restores land beside live data. A PC backup is restored into a new share, right next to the files that were already there.
Downloads repeat. The same installer, ZIP or video is downloaded again because nobody remembers where the first one went.

After a few years, the result is the same everywhere. The volume is almost full, the next step looks like new drives, and nobody knows how much of the data is real and how much is repeat copies. Clearing duplicates first can delay that spend. It also makes the NAS easier to search, quicker to back up and simpler to manage.

Before You Delete Anything: Check These Four Things

A few minutes of checking now saves a lot of regret later:

1. Backups are copies on purpose. Hyper Backup destinations, archive shares and mirrored folders hold duplicates by design. Keep them out of any scan unless you add them yourself.

2. Know where your apps look. If Synology Photos, Synology Drive or a media server points at a specific folder, deleting that copy will make the file disappear from the app. Keep the copy the app uses.

3. Check that the Recycle Bin is on. Deleted files go to a hidden #recycle folder inside each shared folder when Recycle Bin is enabled. That is your safety net, so keep it on while you clean up.

4. Make a fresh backup of anything you cannot replace. Family photos, signed contracts and client work deserve a second copy before any bulk delete.

Method 1: Find Duplicates With Synology Storage Analyzer

Synology gives you a built-in option. Storage Analyzer is a free package from Package Center, and it can include duplicate files in its storage reports. For a first look, it is a sensible place to start.

How to run a duplicate report:

1. In DSM, open Package Center, search for Storage Analyzer, then install and open it.

2. Under Report Profile, click Create.

3. Give the task a name such as Duplicates, then click Next.

4. In the list of report items, tick the option for potential duplicate files, then click Next.

5. Choose the shared folders you want to check. Leave backup shares out.

6. Set a schedule or choose to generate the report now.

7. When it finishes, open the report and go to the duplicates section. You can also export the result to a CSV file.

What to know before you rely on it:

It reports potential duplicates. You decide how strict the match is, for example by ignoring file names or modification time, so a loose setting can group files that are not truly identical.
5,000 file limit. According to Synology's own specifications, each report lists no more than 5,000 duplicate files. On a large NAS, that cap can hide most of the problem.
Manual removal. It does not delete anything. You go through the sets and remove the extra copies yourself.

This is fine for a small share. It gets slow to act on once you have thousands of duplicates.

Method 2: Search by Hand in File Station

File Station has no duplicate finder, but you can still hunt in a focused folder. Open the folder, switch to list view, and sort by size, then by name. Files with the same size and a similar name sitting side by side are good suspects, and you can open both to confirm.

This gives you total control and works well for one messy folder, such as an old Downloads share. It does not scale. A NAS with 400,000 files cannot be cleaned by eye, and size alone can fool you, because two different files can share a size.

Method 3: Find Duplicates Over SSH (For Admins)

If you are comfortable with the command line, you can compare file fingerprints yourself. Turn on SSH in Control Panel, log in as an administrator, and run a command like this on one shared folder at a time:

find /volume1/photos -type f -exec md5sum {} + | sort | uniq -w32 -D

The command fingerprints every file with md5sum, sorts the list, and prints the files that share a fingerprint. Two files with the same fingerprint have the same content, whatever they are called.

A few honest warnings: It reads every file in full, so it puts real load on the disks and the CPU, and it can take a long time on big folders. The output is a plain text list, not a clean review screen. And you should never pipe the result straight into a delete command. Read the list, then remove files deliberately.

Method 4: Use a Dedicated Synology Duplicate File Finder

The fourth route is a tool built for the job. Most general duplicate cleaners ask you to mount or map the NAS as a network drive first and then read file data across your network. DT Synology Duplicate File Finder and Remover is a desktop tool made for Synology. You add the NAS from its Locations panel, so there is no drive letter to map and nothing to copy across first.

How to find and delete duplicate files on a Synology NAS with it:

1. Download and install the tool on your PC.

2. Add your NAS from the Locations panel and sign in.

3. Choose what to scan. Pick the whole NAS, one shared folder, or several folders. Then pick Fast Scan or Deep Scan and start. Watch the live file and folder count.

4. Review the duplicate groups. Every copy of a file appears together with its path, size and date. Decide which copies to remove, remove the extras in bulk, and confirm once.

Nothing is selected for removal until you confirm it, the original copy in each group stays where it is, and removed copies go to the Recycle Bin of the shared folder. During a scan, files are not downloaded to your PC and nothing is uploaded to a Data TB server.

Fast Scan or Deep Scan?

The two modes are a trade between speed and certainty:

Fast Scan compares file name and size. It is quick and catches plain re-copies, like a folder pasted twice or a backup restored over live files. Because it does not read content, it can miss a renamed copy.
Deep Scan compares a file hash, a fingerprint built from the content. It finds true duplicates even when names, dates and folders are different, which is exactly what happens with phone photos and edited exports.

A habit that works for most people: run Fast Scan first to see the easy wins, then run Deep Scan on the folders that matter most, and always before a migration or drive upgrade.

Free scan, paid removal

You can connect a NAS and run a full scan for free, so you see how much space duplicates are wasting before you spend anything. Removing duplicates in bulk needs the full version. There is a 30-day money-back guarantee.

Manual Methods vs a Dedicated Tool

What you need	Storage Analyzer	File Station by hand	SSH command	DT Synology Duplicate File Finder
Built for Synology	Yes	Yes	Works on any Linux	Yes
Match by file content	Potential duplicates, configurable	No	Yes, by fingerprint	Yes, with Deep Scan
Fast name and size mode	Partly, through options	Manual sorting	No	Yes, Fast Scan
Limit on duplicates shown	5,000 per report	None, but very slow	None	No fixed cap for review
Clear review screen	Report only	Folder view	Plain text list	Yes, grouped by file
Bulk removal	No, set by set	No	Only with scripts you write	Yes (full version)
Skill needed	Low	Low	High	Low
Free to try	Included with DSM	Included with DSM	Included with DSM	Free scan

The honest summary: Storage Analyzer is a good first look, File Station is fine for one folder, SSH is for admins who like control, and a dedicated tool wins once the NAS is big and you want to review and remove in bulk.

Why Your Free Space Does Not Come Back After Deleting

This is the part that surprises people. You delete 300 GB of duplicates, look at Storage Manager, and the number barely moves. Nothing is broken. Two things are holding the space:

1. The Recycle Bin

Deleted files take up space until you empty the Recycle Bin of that shared folder. To clear it:

1. Open Control Panel and go to Shared Folder.

2. Select the shared folder and click Edit.

3. Click Empty Recycle Bin.

To do every folder in one go, use Action → Empty all Recycle Bins. You can also set a schedule so old items clear themselves. Only empty it after you have checked that nothing important is inside, because this step is final.

2. Snapshots

If you use Snapshot Replication, past snapshots keep the data blocks of files that no longer exist. Synology explains that simply deleting a file does not remove blocks that are part of a snapshot. Space comes back when the snapshot is deleted or expires under its retention rule.

To see how much space your snapshots use, open Snapshot Replication, go to Snapshots, select a shared folder and choose Snapshot → Calculate Size. To remove snapshots you no longer need, open the Snapshot List for that folder and delete them. Snapshots are your recovery points, so delete only the ones you are sure you do not need.

Also know that Synology says emptying the Recycle Bin may not free space immediately, because the system needs time to reclaim it.

Is Synology Data Deduplication the Same Thing?

No, and the names cause confusion. Btrfs data deduplication works at the block level inside the volume. It stores repeated data blocks once and is only available on certain models and volume setups. Your files still look like separate files, in separate folders, each with its own name.

A duplicate file finder works at the file level. It shows you the extra copies so you can decide which ones to remove. The two do different jobs, and cleaning up duplicate files first is still a good habit, because it makes the NAS tidier for people, not just for the disks.

How to Stop Duplicates From Coming Back

Keep one clear home for photos, and turn off overlapping phone backups to a second folder.
Use shared folders with sensible names instead of personal copies of the same files.
Do not restore full PC backups into a live share. Restore to a separate folder, then move only what you need.
Delete the "just in case" copy after a big edit once you are happy with the result.
Run a scan every few months, so the problem never grows to terabytes again.

Frequently Asked Questions

How do I find duplicate files on a Synology NAS?

You can use Synology's Storage Analyzer package, sort folders by hand in File Station, run a fingerprint command over SSH, or use a dedicated tool such as DT Synology Duplicate File Finder. With the DT tool, you add your NAS, choose the shared folders, run Fast Scan or Deep Scan and review the groups.

Does Synology have a built-in duplicate file finder?

In a way. Storage Analyzer can include potential duplicate files in its reports, and each report lists up to 5,000 of them. It does not remove anything for you, so you delete the extra copies by hand.

Is it safe to delete duplicate files from a NAS?

It is safe when you review first and keep a backup of anything irreplaceable. Check every group, keep one copy of each file, keep backup folders out of the scan, and leave the Recycle Bin enabled until you are sure.

Why did my free space not increase after I deleted files?

Deleted files wait in the Recycle Bin of their shared folder, and snapshots keep the old data blocks. Empty the Recycle Bin, then check Snapshot Replication for snapshots you can delete. It can also take a little time for DSM to reclaim the space.

What is the difference between Fast Scan and Deep Scan?

Fast Scan compares file name and size, so it is quicker but can miss a renamed copy. Deep Scan compares the file hash, so it finds true duplicates regardless of name, folder or date. Use Fast Scan for a quick look and Deep Scan when accuracy matters.

Do I need to mount my Synology NAS as a network drive?

Not for DT Synology Duplicate File Finder. You add the NAS from the Locations panel and sign in. Many other duplicate tools do ask you to mount or map the NAS first.

Can I scan only one shared folder?

Yes. You can scan a single shared folder, a few folders, or the whole NAS. That lets you keep Hyper Backup destinations and other backup shares out of the scan.

How much space can I recover?

It depends entirely on your data. A NAS full of phone photos and project copies often has a lot to recover, while a tidy archive may have very little. The free scan shows the real number before you spend anything.

Conclusion

A full Synology NAS does not always need new drives. Often it needs a clean-up. Find the duplicates, keep one good copy of each, remove the rest in a way you can undo, then empty the Recycle Bin and old snapshots so the space actually returns.

If you want to see how much of your NAS is repeat copies, run the free scan with DT Synology Duplicate File Finder. Nothing is downloaded, and nothing is deleted until you say so.