To understand the difference, consider a different example. You can say either:
I never drink anything but wine. Milk is slimy, and the taste of water is insipid
He took a sip from the chalice. The taste of the water was bitter and chalky.
In the first sentence, you are talking about drinking water generally ("water"); in the second, you are talking about a specific drink of water, which has been referred to earlier ("the water").
Your example is the same, and whether you use "the" will depend on context. You could say either:
I paddled across the lake towards the ruined castle. The darkness of the water chilled my bones.
I looked into her face, her dark eyes reminding me of the darkness of water at midnight.
Both are correct; which one to use depends on the context.