>Is there a method to represent an area of water that is temporary?

For water flow points and lines there are subtypes like

permanent (default), conjectural, intermittent, paleo;  (these don’t all apply to each entity – see the therion book)

There are summer, winter subtypes for air draught points.

 I don’t think this was quite what you are asking, however.

I would tend to draw the passage dry and label it “floods regularly” or draw it wet and label it “often dry”

Bruce