There is roughly 326 million cubic miles (1.34 billion cubic km) of water on the Earth. The original aliens brought 50 motherships that were about 1 mile in diameter each. Individual ships could hold, at maximum, 1/20th of a cubic mile of water (assuming space needed for cargo holds, shuttle bays, engines, quarters and whatnot). Even if the aliens sent an extra MILLION ships (and that's a HUGE exaggeration) to the Earth after the original first series, they would ONLY have taken 50,000 cubic miles of water on that visit alone. While this is, indeed, a lot of water and would have caused notable climate shifts, it would not be more than a drop in the bucket in comparison to the rest of the oceans.
Even with the number of motherships I allow for, the Sirians (Visitors) would need 6,520 trips to haul ALL of it back to their star system. At a 17 year round trip (Sirius and back), it would take 55,400 years just to take HALF of the water on Earth. Then one would have to consider: how could the visitors do without so many ships while at war? Presumably a million ships, with--say--a crew of 20,000 each (total of 20 billion people) would be quite useful in their war against the "bug" aliens.