David Silvester claimed the country had been "beset by storms" since the passage of the new law on gay marriage because David Cameron had acted "arrogantly against the Gospel".
He was suspended by the party after defying a request not to do further interviews on his beliefs following his initial claims made in a letter to a local newspaper.
The move came as leader Nigel Farage launched a clearout of "extremist, nasty or barmy" views from the party ahead of polls in May.
Henley-on-Thames councillor Mr Silvester said he had warned the Prime Minister of "repercussions" if gay marriage had gone ahead and told BBC Radio Berkshire his daily prayers convinced him the recent flooding was the consequence.
He said the new law, paving the way for the first gay marriages in Britain this spring, was the latest mistake which would anger God - following on from abortion laws, which he likened to the Holocaust.
In the radio interview, which followed his initial claims about the link between flooding and gay marriage in a letter to the Henley Standard, Mr Silvester said: "I don't have a problem with gay people.
"I believe as a Christian I should love gay people and indeed, I do. My prayer for them is they will be healed."
The party, which initially supported him after his letter to the Henley Standard, has used emergency powers to suspend him.