From Wikipedia: Some have suggested that the refrain of the song refers to nuclear fallout, however Dylan disputes that this was a specific reference. In a radio interview with Studs Terkel in 1963, Dylan said, "No, it's not atomic rain, it's just a hard rain. It isn't the fallout rain. I mean some sort of end that's just gotta happen... In the last verse, when I say, 'the pellets of poison are flooding the waters', that means all the lies that people get told on their radios and in their newspapers."