That makes it sound easy but...
you can only seal off the cold side then. Because you cant effectively seal off the hot side as well or you won't have a way to cool the hot side of the tec.
And what I am saying is also about the tubes with the water. If the water running through the water cooling tubes is colder than the ambient temperatures, water will condensate on the tubes themselves as well. Unless I am just not picturing a way to completely seal off the tubes as well. That may work, but not sure how you would seal off EVERYTHING that is below ambient temps.
This is becoming hard to theorize things with out pics so...
Throw some ideas on paper so we can more adequately understand what you are trying to do. If you could that would be great.