I definitely noticed a lot of aquatic references throughout the game. Tom has mentioned before that he had planned to make a large ocean-like area. I think I remember him saying it was going to be located on the upper-left of the map, but it was too open and/or didn't really have a point, so it was cut from the final game.
I wonder if the end of the game was going to happen under water?
It could be that the Breach is a form of "ocean". Back when the Rusalki battled in the ocean/Breach, they had a form of insulation against the breach, which was torn apart or otherwise rendered inoperable after they fell to Sudra. Over the years, they forgot the insulation ever existed, and can't access the Breach anymore. It's not too far fetched, considering the Breach in the skies above Kur looks a bit like a boiling ocean.
That said, it's also fully possible that Sudrans were aquatic. Consider that Athetos spread a pathogen designed to kill off Sudrans, and what said pathogen does to survivors, the Sudrans may have mutated into the ghouls, losing their aquatic traits in the process. As for why most bones look humanoid, either the pathogen kills via unstable mutations or the Sudrans have no proper bones to support their aquatic anatomies beyond a humanoid endoskeleton, instead using a far more maintainable "cartilage", or, more specificly, rigid muscle structures, which would be easier and faster to regenerate, to support their fins and flippers. In addition, several areas of the game are more or less inaccessible, or at least difficult to traverse as dry land, even with the planet's weaker gravity - something that isn't an issue if the planet was underwater. It may be that, as the Sudrans believed the Rusalki to be from a sky ocean, they believed the Rusalki to also be aquatic and built the bodies as a gift so they could swim again...only for the idea to fall through when Athetos appeared and one Rusalki sided with him.