I think it is pretty obvious that humans are more water-friendly than most other apes. However, the most likely explanation for this is that humans invaded water environments much as they invaded every other habitat on the planet - by using cultural transmission to adapt to these environments while also shielding themselves from their more negative aspects.
That humans are cultural apes is pretty uncontroversial. Cultural transmission explains practically every difference between humans and chimpanzees. It seems likely that it also explains those differences associated with adaptedness to aquatic environments.
Cultural transmission of traits that help with survival in the water are well known, and have been observed in primitive tribes. Cultural transmission of swimming, diving and breath holding are all old phenomena. Similarly many of the negative aspects of oceanic environments can be protected against using cultural transmission. Drowning can be learned about; sea predators can be defended against, hypothermia can be avoided or treated - and so on.
Some aspects of these behaviours fossilize. For example, we can be pretty sure that humans have been diving for pearls for thousands of years - because we can see the resulting pearls. We also know some things about the rafting feats of early humans - through looking at the geographic distribution of human genes in islands. We know roughly who rafted where and when. Modern humans don't normally get onto ocean-faring rafts unless they can swim pretty well.
I think that cultural evolution is a sufficient explanation for human traits associated with water-friendliness. For example, there is no pressing need to invoke any environmental flooding to explain why humans are as water friendly as they are. Also, the idea that watery environments led to bipedalism (through the need to keep the nose out of the water) is weakened by the cultural explanation. Cultural transmission explains most of the observed facts without invoking this particular speculation. Instead cultural transmission led to bipedalism too.