Her Majesty will be welcomed to Glenmuick Church in the Cairgorms where she will also meet firefighters, police and other community members who helped lead a response to the crisis last December.
Rev David Barr told Premier: "The whole village is truly honoured that her Majesty has asked to come and it's a great honour."
Around 600 homes and 100 businesses around the nearby village of Ballater and surrounding areas were devastated as floodwaters ensued, according to Aberdeenshire Council.
The River Dee burst its banks during the storm and nine months later businesses along Bridge Street in Ballater are still rebuilding and repairing.
With her private residence in Scotland, Balmoral Castle, a short distance away, the Queen will also visit a caravan park damaged by floodwaters and a newly-reopened golf course.
The Queen, who celebrated her 90th birthday earlier this year, has spoken publicly about the role Christian faith plays in her life, describing it during her 2014 televised Christmas message as "an anchor in my life."