It is hinted upon. The Mariner's special physiology is due to genetic engineering since it's only been 500 years since the world got covered in water it would have been believable if it was 50,000 years.
shareIn what way was it hinted upon?
shareIt has only been hinted at being a mutation and it never says how long after the flood it is
shareThe term 'mutation' as bandied about in 'Waterworld' is deliberately misleading and suggests human agency, whether by chance (as in the effects of a nuclear holocaust), or by choice (experimentation, or genetic engineering). 'Mutants' are shunned and destroyed by the inhabitants of the Atolls in a manner that suggests a mass rejection of some past terrestrial cultural behaviour, contemporaneous with whatever event caused the Flood. Even Old Gregor, the only thing in this film passing for a scientist, seems slightly dubious about the Mariners' features being naturally evolved. From a more scientific viewpoint the idea of a natural mutation or evolution is unlikely, given that humanity is in a state of sharp population decline, a condition that would tend to discourage such change.
Further, the Mariner seems to be what 19th-century pseudoscientists called an atavism, or throwback: in very much the manner of his own unremembered ancestors leaving the seas to become land-based creatures, the Mariner has gone back to the seas, and become an aquatic creature once more. This is one of several broad philosophical themes that are explored in this film.
It's unlikely that humans would develop gills. Compare to the situation of marine reptiles and mammals such as dolphins. If mankind were to adapt to a aquatic life we'd probably stay air-breathing, but develop our lung capacity, streamline our shape, and eventually develop flippers. The jump to gills is too big, and evolution tends not to do that.
Genetic engineering is a possibility. I don't see that as being incompatible with the mariner being called a 'mutant'. Society has broken down, effectively, and they may not even remember (or know) where the mutants came from.