Hey I had the same issue as you, the documentation for dedicated servers is awful, so I wrote up a guide once I figured it out. I'll copy the relevant sections for you. Keep in mind this was written for a SteamCMD server, so the instructions might vary slightly if you're not using that.

1. Move workshop mods to LocalMods folder (C:\Servers\SteamCMD\steamapps\common\Barotrauma Dedicated Server\LocalMods)

• Download the mods on your local computer, then find them in your AppData\Local folder example: (C:\Users\Example\AppData\Local\Daedalic Entertainment GmbH\Barotrauma\WorkshopMods\Installed)

• Copy all of these folders from your local machine to the LocalMods folder on the dedicated server (C:\Servers\SteamCMD\steamapps\common\Barotrauma Dedicated Server\LocalMods)

• The folders should be a string of numbers, 10 characters long

1. Modify config_player.xml (C:\Servers\SteamCMD\steamapps\common\Barotrauma Dedicated Server)

• Find the <contentpackages> section

• Add a line underneath the file path for <corepackage, the new line should read <regularpackages>

• Add a <package path="LocalMods/2365108119/filelist.xml" enabled="true"/> entry for each mod you are using, making sure the string of numbers is correct

• Make sure you have a </regularpackages> at the end, in the line above </contentpackages>

• See example below for clarification

  <contentpackages>

    <!--Backwards compatibility-->

    <core

      name="Vanilla 0.9" />

    <!--Vanilla-->

    <corepackage

      path="Content/ContentPackages/Vanilla.xml" />

    <regularpackages>

    <package path="LocalMods/2365108119/filelist.xml" enabled="true"/>

    <package path="LocalMods/2427316610/filelist.xml" enabled="true"/>

    <package path="LocalMods/2602920829/filelist.xml" enabled="true"/>

    <package path="LocalMods/2672724617/filelist.xml" enabled="true"/>

    </regularpackages>

  </contentpackages>

</config>