I'm currently voting 2-1 Vienna seemingly alone. Probably fair, and if someone is going to make the case for Wroclaw then I will probably change my vote.
Meanwhile, Vienna has quite a few aquatic exhibits.
First and foremost, the Aquarium-Terrarium House has a variety of fish and reptiles. Highlights for me were the enclosures for Morelet's crocodile, caiman lizard and stingrays, anaconda, and the small reef tank. There's also a heavy focus on rare fish, with a couple of rare fish tanks (which in itself are nothing special). Still, a cool addition. Outside, there are small terrariums for a few native amphibians, as well as an enclosure for flamingos.
Vienna's polar bear habitat called Franz-Josef Land is the best I've seen.
The Polarium houses aquatics as well: South American sea lions, northern rockhoppers and king penguins, as well as Humboldt penguins nearby.
The Rainforest House most notably has the
Frogs & Friends exhibition, displaying two Staurois species, both of which Vienna has basically established in Europe. Also displayed here are vampire crabs, northern river terrapin (one of two European holders and first captive breeder), mudskippers, three species of treefrog, Asian small-clawed otters, eyespot pufferfish and giant gourami.
Aside from those four major displays, the zoo also houses common hippopotamuses, another species of flamingo, a few aquatic birds and amphibians in the bird house (sunbittern, African bullfrog, strawberry poison dart frog, African jacana, wattled jacana, dyeing poison dart frog), water buffalo, capybara, maned duck and a couple Eurasian waders in a European-themed aviary (pied avocet, little bittern, Eurasian teal).
Finally, Vienna also contributes quite a bit to aquatic species conservation and research. They set up conservation initiatives for the northern river terrapin in Bangladesh and India, support Polar Bears International, protect European pond turtles in Austria, keep and breed no less than 18 species of threatened Aphanius species (two of which are currently EW), and breeds and protects the European mudminnow (a species once thought extinct in Austria). They research communication in the two species of rock frogs and the occurrence of chytrid fungus in Austria.