Much like Halley's Comet as described in last week's Cosmos, early humans ascribed cosmic phenomena to the whims of some heavenly god... when in actuality, it was just a comet. I bet that origins of the Noah's Flood story come from an actual event. There probably was some kind of flood, and it was probably catastrophic, but by no means was it all-encompassing and worldwide. It was embellished to the story we have today.
One of the more likely candidates is
the Black Sea deluge hypothesis in which the Mediterranean catastrophically breached through the Bosporus to pour into the Black Sea with the flow of 200 Niagara Falls. At the time (somewhere between 7800 and 5600 BC) the Black Sea shorelines were occupied (possibly densely), and the remains of human structures have been found about 100 meters below the current water level.
If this were the source of the flood story, then someone probably noticed that the Med was starting to pour in (cutting a deeper and deeper channel as the trickle turned into a stream) and tried to warn people living below. One of them then built a boat or raft large enough to hold his family, sheep, and goats and floated around on the Black Sea as he watched the local villages disappear under water, never to be seen again. Meanwhile the steam from the giant falls would've fallen as enormous amounts of rain. The boat would've made landfall far inland from the areas that had been inhabited, so the survivor would've found the Earth "depopulated."
Whether people would keep jabbering about such an event for thousands of years afterwards is a big question, but the entire region seems to have different versions of a giant flood story.