Its 200th anniversary is on Thursday and marks the final defeat of the Emperor Napoleon, in a battle that cost some 25,000 British and allied lives.
The prince will perform the unveiling ceremony on the Belgian battlefield reports BBC.
More than 5,000 enthusiasts in period uniforms are at the battle site, ahead of a two-day re-enactment this week.
The BBC’s Nick Higham says many are camped next to the farm at Hougoumont, a strongpoint in front of the Duke of Wellington’s allied army, and scene of some of the fiercest fighting of the day.
The prince and the Duchess of Cornwall, along with Belgium’s Princess Astrid, will tour Hougoumont farm, which has recently undergone a £3m project to restore it, following years of neglect.
It will be officially opened on Wednesday.
The new memorial shows two life-size soldiers struggling to close the north gates of the farm, to save it from being overrun by the French.
This defence of the farm was so important that Wellington later said the outcome of Waterloo “turned on the closing of the gates at Hougoumont”.
On one of the stone gates are carved words from the Duke’s official despatch after the battle: “The army, on any occasion, never conducted itself better.”
On Thursday there will be a national service at St Paul’s Cathedral to commemorate the anniversary.