There is a formal design layout by William Walker in 1764 and there are some survey plans of the estate in 1817 & 1825, carried out by William Crawford.
Part of the estate was originally known as Priestfield, dating from the times when it was owned by the monks of Kelso. The lands were later acquired by the Hamiltons and were bought from Sir Thomas Hamilton in 1672 by James Dick, created a baronet in 1677. Sir James later bought the land of Craigmillar from one Preston and, in joining the two estates, named them Prestonfield. Sir James was one of the first land improvers in the neighbourhood, and set about draining and enclosing the fields, cleaning the streets of Edinburgh City (of which he was Provost) at his own expense, and using the manure to fertilise his lands. Before these improvements were made, the area had been covered with scrub oak woods, the hiding place for Edinburgh's 'thieves and lymmars' and one of the meadows was famed as a duelling ground.
Sir James was an Episcopalian; however, in 1681 his house was burned down by students from Edinburgh in an anti-catholic riot. Money was approved in theory from the public purse in recompense but, in practice, was not available. However, Sir James started the rebuilding of a new house in 1687, commissioning Sir William Bruce who had just completed work at the Palace of Holyroodhouse. Sir James was friendly with Charles II's brother, the Duke of York (later James VII of Scotland & II of England) who lived at Holyroodhouse at this time and it is reputed that a path leading from the Palace to Prestonfield was known as the 'Dukes Walk'. The new house incorporated a little of the former tower, and was built in a domestic style. The initials SJD and DAP, (for his wife Dame Anne Paterson) are carved above the upper windows. Sir James improved his lands to the extent that he recorded selling surplus produce from his vegetable garden. Seed catalogues dating back to 1690 have been found at the house, advertising fruit trees and seed. He died in 1728 and was succeeded by his daughter Janet, who had married Sir William Cunyngham of Caprington; their younger sons, on succeeding to the Dick Baronetcy, adopted the name Dick.
Sir Alexander Dick succeeded his elder brother in 1748. He was a famous physician, for many years President of the Royal College of Physicians. He also entertained many of the famous writers and philosophers of the day, including the Allan Ramsays, Hume, Boswell and Johnson. His great-niece, who visited and wrote about Prestonfield, was Lady Anne Lindsay, the poetess. Sir Alexander put in a canal, dredged marl from the loch, planted many trees in the policies, including the yellow 'Lorraine' planes, and he is also recorded as laying out the long grassed walks, planted with snowdrops, crocuses and daffodils. In 1774 he was awarded the Gold Medal of the Royal Society of Arts for the cultivation of a strain of rhubarb for medical purposes (thus apparently saving #s in imports) It was a strain imported from Dr Maunsey of St Petersburg, which had originally come from the Great Wall of China. Hemust also have cultivated mushrooms, as he recorded that he breakfasted each day on mushrooms stewed in cream; the growing of nectarines, peaches, figs grapes and melons is also recorded. Sir Alexander died in 1785 and was succeeded by his son, Sir William. Lord Cockburn's memorials record that in Sir William's time, 'the weeds on Duddingston Loch were regularly cut over by means of short scythes, and this made the loch nearly twice its present (1856) size. Between the loch and the house was a sort of Dutch Garden admirably kept. Besides the bowling green, it had several long smooth lanes of turf, anciently called bowling alleys, parterres and lawn interspersed, fountains, carved stone seats, dials, statues and trimmed evergreen hedges. How we used to make the statues spout! There was a leaden Bacchus in particular, of whose various ejections it was impossible to tire. A very curious place.'
In the early 19th century, Sir Robert Keith Dick built a new circular block of stables on the site of the old Dutch Garden and turned the remnants of the garden into grazing land for his stud horses. The new kitchen garden was put in to the south of the house, and the old one put to grass. The Bacchus was relocated in the 1880s, having resided in the stables for the previous three generations. It is now on the terrace south of the house. Sir Robert extended the house at about the same time, building on the two oval rooms on the south facade, and adding the portico.
Few changes have been made to the layout since that time; Sir William Stuart Dick- Cunyngham planted a grand show of daffodils along the main drive in the 1920s. The rose beds were put in c.1935, and the present layout of the shrubbery was designed by Mrs Janet Dick-Cunyngham in the 1960s.