The story in the Vedas probably has the same origin as the Mesopotamian flood myths. The oldest surviving Akkadian and Sumerian references to the flood precede and are pretty close in time to the Aryan expansion to the Indian subcontinent, and the Mesopotamian cities had long-lasting trade, cultural and military links to the peoples living in the Iranian plateau.

I love speculating on the origin of the flood myths. My personal favorites are long-lasting oral traditions about the Black Sea flood and the Persian Gulf flood, both of which were rapid, catastrophic large-scale floods of large areas that were previously settled by humans. Sadly, the true origin is probably a lot more banal -- the oldest surviving fragmentary literary evidence refers to the specific city that flooded, Shuruppak, or modern Tell Fara. There is indeed a significant flood layer there (60cm of alluvial sand!) at about the right time (2900BC), but this was left by a normal river avulsion that created a violent but local flood.