This Bob Dylan song comes from Ferry's 1973 album of covers These Foolish Things. As his first solo single, it reached no. 10 in the UK charts the following year.
I have always assumed the hard rain was nuclear fallout, but in a 1963 interview (says Wikipedia) Dylan told Studs Terkel:
"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."