Under the early Tudor kings magnificent royal palaces were constructed in northern Surrey, in convenient proximity to London. At Richmond an existing royal residence was rebuilt on a grander scale under King Henry VII, who also founded a Franciscan friary nearby in 1499. The still more spectacular palace of Nonsuch was later built for Henry VIII near Ewell. The palace at Guildford Castle had fallen out of use long before, but a royal hunting lodge existed just outside the town. All these have since been demolished. Surrey's cloth industry declined in the sixteenth century, and effectively collapsed in the early seventeenth. However, this period also saw the emergence of important new industries, centred on the valley of the Tillingbourne. The manufacture of copper and brass goods in this area in the sixteenth century proved short-lived, but in the seventeenth more durable industries were established, producing paper and gunpowder. The Wey Navigation, begun in 1635, was one of England's first canal systems.

Surrey almost entirely escaped the direct impact of fighting during the main phase of the English Civil War. The local Parliamentarian gentry led by Sir Richard Onslow were able to secure the county without difficulty on the outbreak of war. Farnham Castle was briefly occupied by the advancing Royalists in late 1642, but was easily stormed by the Parliamentarians under Sir William Waller. During a political crisis in summer 1647 Sir Thomas Fairfax's army passed through Surrey on its way to occupy London, and subsequent billeting of troops in Surrey caused considerable discontent. In the brief Second Civil War of 1648 the Earl of Holland entered Surrey in July hoping to raise a Royalist revolt but found little support. After confused manoeuvres between Reigate and Dorking as Parliamentary troops closed in, his force of 500 men fled northwards and was overtaken and routed at Kingston.

Surrey had a prominent role in the development of the radical political movements unleashed by the civil war. In October 1647 the first manifesto of what became known as the Leveller movement, The Case of the Army Truly Stated, was drafted at Guildford by the elected representatives of New Model Army regiments and civilian radicals from London. In 1649 the Diggers led by Gerrard Winstanley established a communal settlement at St. George's Hill to implement their egalitarian ideals of common ownership, but were eventually driven out by the local landowners through violence and litigation. A smaller Digger commune was then established near Cobham, but suffered the same fate in 1650.

The sixteenth century is the earliest from which a sizeable amount of non-military secular architecture survives in Surrey. Important examples include the grand mid-century country houses of Loseley Park and Sutton Place and the old building of the Royal Grammar School, Guildford, founded in 1509. A considerable number of more ordinary houses and commercial buildings of the sixteenth century are also still standing, and with the seventeenth century the number of surviving buildings proliferates further. Abbot's Hospital, founded in 1619, is a grand edifice built in the Tudor style, despite its date. More characteristic examples of major seventeenth century building include West Horsley Place, Slyfield Manor and the guildhall in Guildford, as well as Ham House and Kew Palace, formerly in Surrey but now in Greater London.