What is the difference between "dewatering" and "unwatering"

Solution 1:

The Corps of Engineers uses the term unwatering to describe removing water from locations where it is not supposed to be (subway tunnels, house basements). Dewatering describes removing water from locations where it is usually located (inside locks, river beds).

Reference: http://www.capradio.org/news/npr/story?storyid=163988271

Solution 2:

Dewater is the usual verb that has the meaning to remove water (from).

By contrast, like many other such words, unwater more often appears in the past tense as an adjective, rather than by itself as a verb. An unwatered plant is one that has not been watered.

Usages such as (to) unwater (something) or unwatering something always sound odd and out of place, though not rare. Some dictionaries have defined unwatering as akin to dewatering.

Referring to the process of removing water as unwatering as you stated the article does, is to focus on the context: dewatering relates closely to the process, unwatering would draw attention to the site ('rendering the site better by removing water'). This is kind of a semantics-pragmatics technique. Journalese is full of such.