The land and mills of Bonnytoun formed part of the Barony of Broughton mentioned in King David I's confirmation charter to the Abbey of Holyrood in 1143.
The village suffered in 1544 when the Earl of Hertford's army passed through on its way to attack Edinburgh and again in 1547 after the Scottish defeat in the Battle of Pinkie, both events in the period of conflict known as the Rough Wooing.
At the Council's invitation, a Dutchman Jeromias van der Heill was installed in 1621 as a dyer to teach his craft locally.
When the mill buildings were demolished in the face of local protests in the 1980s, the house was saved, restored and converted into private apartments.
One of the larger developments in the area from the 1980s is the storage depot of the John Lewis Partnership in Bonnington Road Lane (this includes a minor public pick-up counter for some items).
New housing built along the river bank has changed the face of the area around Bonnington Mills and necessitated work on improving flood defences.