Really good question. Here is my explaination.

Moeritherium, researchers now believe, retained the basic skeletal architecture of a terrestrial browser even as it grew increasingly (i) _______ a partially submerged existence along ancient riverbanks. The skull's eye sockets, positioned unusually high and close to the top of the head much like those of a hippopotamus, imply the animal habitually kept most of its body (ii) _______ while only its eyes and nostrils broke the surface. Its dense, heavy limb bones, meanwhile, would have offered little buoyancy and were almost certainly (iii) _______ any sustained swimming.

Even as it grew + Partially submerged existence along ancient riverbanks. - This sentence suggests we are dealing with an animal that spent most of it's time underwater.

For this context, hence B would be appropriate. "Habituated to" because the animal specie here is not originally a part of that atmosphere (clue : terrestrial browser), but got habituated to a water body like atmosphere.

If you know anything about hippopotamus, it is that their eyes are at the top, making it easy for them to see whilst they are underwater. The author here, tries to compare the said animal to the hippopotamus here.

Given this clue + "most of the body", implies the animal was subsumed into something, unlike the way it normally carries itself.

And for the last blank, since it has "little buoyancy" which basically means it is not able to float properly, the body's weight is essentially hindering it from its ability to float. Hence, "hindrance to" is the most apt option here.