During January, each shopper is asked to drop a token into one of three collecting bins representing each charity.
At the end of the month, £1000 is distributed between the charities in proportion to the number of tokens received.
British Deer Society spokesman, David Kenyon, said: “Waitrose has long supported sales of venison and game meat but this is a new departure for the company. If you are in the Salisbury area in January, drop in to Waitrose and drop in your token to support the society.”
The Waitrose funds will be used to support the Deer Vehicle Collisions campaign Look out for Deer.