Like Pokemon Go? They’ve got sea creatures floating over land. I don’t like that idea for this game, though.
The best way I can think of for implementing aquatic creatures is to only gather their DNA through incubators or special events. I’m not sure I’d even much like the idea of them spawning everywhere there’s water, like they have in PoGo. A Mosasaur in an 8-feet-wide creek? Wouldn’t be that bad, but kinda iffy. And if aquatics are worth using (which they’d have to be), it’d be unfair to the people who live at landlocked deserts.
An aquatic-only arena I could imagine. Or there could occasionally be rare special events where everyone (or an alliance all together) fights a giant aquatic creature, and everyone’s sending their land dinos against an aquatic reaching out of the tank/beach/whatever. If you have an aquatic creature, it would only be useful in specific water battles or this special raid event.