The pond was simply a spontaneous idea by Waffle when he got his hands on a jackhammer.
While the pond was a success among the newts, Blik wanted the pond gone. Waffle had run this through his robot clone, but the clones accidentally fell into the pond, short-circuiting all three of them.
After further events, the entire mansion was torn down, taking the pond with it. The mansion was immediately rebuilt, but the pond wasn't restored.
It is unlikely if the Newt Pond will ever get another chance in the mansion, so Waffle's newts had later moved on to swimming in the toilet. A dangerous resort, as Mr. Blik had shown the will to flush the little newts down the toilet before.