Fishing through the links mentioned over at Christianity SE, I netted this scientific paper about freshwater and marine fish: Why are there so few fish in the sea?. Apparently the bulk (96%) of marine species have a single freshwater ancestor species extant 300 Mya (300 million years ago). Descendants of this species did not enter the ocean until about 180 Mya, with the greatest diversification and subsequent dominance of the oceans starting 110 Mya. Another fact: only 4% of current fish species can thrive in both saltwater and freshwater (e.g., salmon, trout, ...).
To get anywhere near a hypothetical event equivalent to Noah's flood would require accepting dozens of counterfactual assumptions, and a total misunderstanding of geology, evolution, paleontology, not to mention conservation of mass (where did all the water come from?).
But to address the narrow issue of survival of fish, one could imagine that the flood happened so rapidly as to create a very thick layer of freshwater on top of the saltwater. Freshwater is considerably lighter than saltwater, and would "float" on the saltwater. Marine mammals would be okay in freshwater for a few days. Then the waters could recede (where did all the water go to?), and maybe enough freshwater species would end up in the new freshwater lakes and streams.
As far as the Ocean being less salty, there is no evidence for that. A lower salinity is postulated to fit into the theories of the Young Earth proponents. Paleosalinity is a complex study. You can browse through these references here and here.
A flood such as this would have enormous, I would say overwhelming, geological, geographical, and paleontological evidence left behind, which in fact does not exist. But everything is possible with miracles.
You may be interested in this paper: An Abrupt Drowning of the Black Sea Shelf which led to this book NOAH'S FLOOD: The New Scientific Discoveries About the Event That Changed History