The original masons used local granite for strength and Elgin sandstone for the carved facings, which was easier to work and could be cut into the heraldry of bishops, kings, and Aberdeen's own coat of arms. Their bridge served until 1718, when nearly the whole structure was rebuilt — the original 16th-century piers were retained, but most of the arches above were laid again from scratch. Another major change came in 1841, when the city architect John Smith widened the deck from fourteen feet to twenty-six, almost doubling it to accommodate increasing traffic. The original piers still carry the weight. The carved coats of arms still face the river. The small passing places along the parapet — built for foot traffic to step into when a cart came by — are also still there. The bridge was designated Category A listed in 1967 and was a Scheduled monument until being de-scheduled in February 2009. Today it carries the A92 trunk road from Stonehaven and points south.

Twice in its early life the bridge became a focal point of national politics. On 17 April 1589, George Gordon, sixth Earl of Huntly, marched south from Strathbogie with his Catholic supporters and met King James VI here. There was no battle — Huntly surrendered a few days later — but the bridge had served as the natural meeting place between a rebellious north and a royal south. Fifty years later it became a battlefield. On 18 and 19 June 1639, the Royalists under James Gordon, Viscount Aboyne, defended the bridge against the Covenanters under the Marquess of Montrose and William Keith, 7th Earl Marischal. It was the only serious military engagement of the First Bishops' War, and it produced one of the strangest historical footnotes of the period: the battle took place after the peace treaty had already been signed. The news from Berwick simply hadn't reached Aberdeen yet. A contemporary verse survives, equal parts mocking and devout: 'Muskies mother has made a vow, That she will take her venter, And thunder throughe the brige of Dee, Led by a Covenanter.' Muskies mother was a large cannon.

A chapel once stood beside the bridge — a resting place for pilgrims travelling to and from Aberdeen. No record survives of when it was built, but in 1530 it produced a peculiar legal dispute. Gordon of Abergeldie petitioned the Aberdeen town council on 27 February, claiming the chapel was blocking access to his fishing rights in the river. The council heard him out and decided against him. Gordon, frustrated, took matters into his own hands: he simply removed one of the bridge's buttresses to clear a footpath for his men down to the river. Aberdeen Town Council, who owned the bridge, retaliated by suing him in the Edinburgh High Court. The chapel is long gone. The buttress was eventually replaced. But for one year in the early 16th century, a fishing dispute literally damaged the city's southern gateway.

Until 1832, the Brig o Dee was the only way to enter Aberdeen from the south. It sits at the northern terminus of the Causey Mounth, the medieval drovers' road that lifted travellers above the worst of the bogs between Aberdeen and Stonehaven, passing Bourtreebush and Muchalls Castle along the way. This was the route Montrose and Earl Marischal followed in 1639 with their nine-thousand-man Covenanter army. It was also the route along which generations of cattle drovers, mail coaches, lairds, soldiers, and ordinary travellers made their first entry into the granite city. The bridge survives all of it, widened but not replaced, still on its original piers, still carrying the main southern road into Aberdeen as it has done since the year Henry VIII was looking at his second divorce.