Whenever you create a new file in GoldSim while the Contaminant Transport Module is enabled (or if you enable the Contaminant Transport Module in an existing file), you will find a Container named "Material" in the Model Root.
This Container contains two elements: the Species element, and the Reference Fluid (named "Water"):
This Container is created only for your convenience. If you want to, you can move these elements out of the Material Container to some other location, and you could then delete the Container. You can also rename the Reference Fluid "Water" to something else (e.g., Blood, Air). Note, however, that GoldSim will not allow you to delete either of these elements.