The merpeople evolved from humans.
I have only started the game, so I don't know if this theory is contradicted somewhere. However, flippers, unlike fins, are a feature found on aquatic descendants of land-dwelling species. From this we can infer that while "classic" mermaids are likely to have evolved underwater, Naija's species is more likely to have descended from land-dwelling humanoids, having mostly human features with flipper feet.
- The ending reveals that all creatures in Aquaria were created by a human boy who fell into the ocean and somehow obtained godlike powers. Naija's mother was a first generation created entity. It's far more likely that the boy simply used humans as a template and slapped flippers and gills onto them to create marine life that he could relate to.