When the file system runs out of space there will be a dramatic decrease in query performance and merges will cease.  There will also be a number entries in the ErrorLog.txt file that look like these:
 

Mitigation

1. Move/Remove any unwanted files from the file system. This might include cleaning up log files that have grown very large.
2. Add additional storage to the host.  This may require that you move the location of forest data. 
   For more details, please refer to the below documentation pages:
   - https://docs.progress.com/bundle/marklogic-server-administrate-12/page/topics/database-rebalancing/overview-of-the-database-rebalancer.html
   https://docs.progress.com/bundle/marklogic-server-administrate-12/page/topics/database-rebalancing/retiring-a-forest-from-the-database.html

In the event that the data directory containing the forest data and the directory containing the MarkLogic config files are on the same partition (which is common on Windows installations), it is possible to encounter a unique situation. In this situation, if the file system is completely full, MarkLogic will be unable to write config files. If this condition occurs, no tasks can be performed using the Admin UI. In this situation, the forest data must be moved manually if insufficient disk space can be freed to allow configuration files to be written. This is a special‑case procedure and is not recommended when the Admin UI is accessible.  
 

Step 1. Stop MarkLogic
 

Step 2. Move the forest data to another location.  Be sure to maintain permissions assigned to the forest data.
 

Step 3. Start MarkLogic
 

Step 4.  Detach the forest from the DB
 

• In the Admin UI navigate to Configure -> Databases -> [Database-Name] -> Forests
• Uncheck the box next to the forest and click "OK".

Step 5. Create a new forest, specifying the new storage location

• In the Admin UI navigate to Configure -> Forests
• Click the "Create" tab and fill in the appropriate information

Step 6. Copy all data from the old forest directory into the new forest directory

Step 7.  Attach the new forest to the DB

• In the Admin UI navigate to Configure -> Database -> [Database-Name] -> Forests
• Check the box next tot the newly created database and click "ok".

Step 8. Ensure there were no errors while mounting the new forest

• In the Admin UI navigate to Configure -> Database -> [Database-Name] and click the status tab
• It is also a good idea to look for any errors in the error log (For example, for Linux in /var/opt/MarkLogic/Logs/ErrorLog.txt)

Step 9. Provided there were no issues with the new forest, the old forest may be deleted

• In the Admin UI navigate to Configure -> Forests -> [Old-Forest]
• On the "Configure" tab select delete.
• The old forest data will need to be deleted manually.

References to Other documentation:

Memory, Disk Space, and Swap Space Requirements
https://docs.progress.com/bundle/marklogic-server-install-12/page/topics/requirements-and-database-compatibility/memory,-disk-space,-and-swap-space-requirements.html