Evaporation

From DwarfFortressWiki

Water (and, oddly, magma) with a depth of one will slowly disappear. Outdoor water of any depth will evaporate (and possibly disappear completely) during hot or dry seasons.

Deeper water seems to lose water at a slower rate: Observed a depth 2 pool vanish completely while a depth 5 pool didn't lose any water at all, over a couple seasons.