Last week the Football League said it was investigating the Premier League club for allegedly supplying false financial information.
The Telegraph said it obtained a forged bank letter submitted when Gino Pozzo became owner before the 2014-15 season.
Riva said: "I fully refute, and will protect vigorously my integrity against, any recent speculation."
Watford, who won promotion from the Championship in 2014-15, could have points deducted or be fined if they are found to be at fault.
Riva, who replaced Graham Taylor as chairman in July 2012, said: "For the past four years I have acted with honesty and in good faith in all my dealings on behalf of the club, and the club has developed and grown a great deal in this period."
Watford chairman Raffaele Riva has stepped down after four years in charge to focus on "other business interests".