If it's based on a real flood, they presumably follow a power law distribution, where you have relatively frequent "normal" floods, and progressively larger floods are rarer and rarer, till you get an occasional gargantuan one.
My guess though is it's probably a plot device where the storyteller takes a known phenomenon and just exaggerates it to magical-mythical proportions, which may contribute to the story being repeated as it strikes the balance between the relatability of the real phenomenon and the attention-grabbing otherworldliness of its exaggerated version.
For the same reason people in places where it snows every year still remember the really big blizzards: some floods are worse than others. Any given generation will have a flood they recall that set the (ahem) high water mark for comparison to future floods.
I don't know, if I know it floods every year, and there is a really big flood, I don't think I would act like the flood was something completely out of the blue. I would probably mention how it was much bigger than the normal floods.
For that reason, I think an event completely different from the yearly flooding is more likely, for example the Minoan eruption or Black Sea deluge hypothesis.
I have often wondered if these flood stories document something much larger that might have occurred as the major ice sheets collapsed and raised the sea levels to unseen heights.
But the one that is most intriguing IMHO is the mediterranean sea event that happened but it is 6M years ago. Could ancestors of genus Homo have passed that story long for all that time even across speciation???
My guess though is it's probably a plot device where the storyteller takes a known phenomenon and just exaggerates it to magical-mythical proportions, which may contribute to the story being repeated as it strikes the balance between the relatability of the real phenomenon and the attention-grabbing otherworldliness of its exaggerated version.