William Younger, with their Holyrood and Abbey breweries was the most famous, but there were many others. Including Drybrough and Bernard, who were closer to Waverley Station. Rather too close, as it turned out:
"THE RECONSTRUCTION OF THE WAVERLEY STATION.Here's a map showing the area affected. The building in the centre of the picture marked "brewery" is Drybrough. It looks like the railway line passes right through it. The big building to its left is the grain store mentioned in the article. The building with the "H" of South Leith on it on the other side of the road is Bernard's original brewery.
Another important stage in the work of reconstructing and enlarging the Waverley Station, Edinburgh, and its approaches has been reached by the completion of the new double line of rails between Waverley and Abbeyhill, and of the new up main line platform. To-day these additions to the undertaking come into operation, and it is manifest from the size and situation of the new permanent works that the increased facilities they afford for the conduct of the traffic to and from the east and south will be of immense advantage and convenience, not only to the railway officials, but also to the travelling public. This new portion of the line lies to the north of the present railway. Its construction involved the removal of, among other buildings, a large grain store, and Drybrough & Bernard's breweries, and the setting back of the North Back of Canongate to the foot of the Calton rock. It also involved the cutting of a new tunnel through the Calton Hill, and the carrying of the double line of rails to Abbeyhill Junction. Extensive operations were thus necessitated over a large area, but the work has been pushed forward with great celerity by the North British Railway Company's engineers and contractors. Most passengers who travel to the south and east have experienced the discomfort of boarding a train in the narrow, draughty archway formed by the north abutment of the Old North Bridge. The abutment is now in course of demolition, and its removal will be followed by the widening of the "up" or north platform, in accordance with the plan of the new permanent works."
Evening Telegraph - Monday 26 April 1897, page 3.
It's clear that Drybrough's brewery was right in the way of the railway. Presumably the enforced demolition of their brewery was a good chance to escape to a less crowded part of the city with more room for expansion. Duddingston, with its water supply and railway connections, was the perfect choice.
What's surprising is that the largest of the Old town breweries, William Younger, was the last to disappear. Not moving, of course, but just closing.
Demolition couldn't have been too big a problem for Bernard. They'd already built a new brewery on the Slateford Road some years earlier.