The 91-year-old monarch was presented with a specially-labelled bottle of Highland Spring water she helped make after pressing the button to start the new production line.
The commemorative bottles have a crown on the thistle logo and the slogan 'Specially selected for Her Majesty the Queen'.
Producing more than 20 bottles per second, the new production line is the fastest of its type in the UK and is part of a £30 million factory extension.
The royal arrived at the factory in Blackford, Perth and Kinross, to the sounds of a piper and was met by the Lord Lieutenant of Perth and Kinross Brigadier Melville Jameson, the firm's owner His Excellency Mohammed Mahdi Al-tajir and chief executive Les Montgomery.
Mr Montgomery showed the Queen the source of the water in the Ochil Hills from a viewing balcony before she was given a tour of the bottling hall, met staff and workers, and unveiled a plaque to mark her visit.
Group operations director Bryan McCluskey showed the Queen around the factory and explained the bottling process, describing the visit as an 'enormous honour'.
He said: 'Having the longest-reigning monarch coming to see the fastest bottling line in the UK was amazing. She was really interested and could quote some of the statistics she had heard.
'She was very impressed with the new bottle design and we presented one of the new bottles to her which she had effectively made.'
She was also presented with a silk scarf in Highland Spring tartan.
Before leaving, the royal greeted crowds waving Union flags and was presented with floral posies by Mr McCluskey's daughter Lucy, nine, and Sophie, eight.
Her Majesty and the Duke of Edinburgh are spending Holyrood Week - known locally as Royal Week - visiting various regions around Scotland, meeting subjects across all walks of life and hosting thousands at Holyrood Palace.