Waterford is, historically, the capital of County Waterford in Ireland, though today the city is administered separately from the county, the latter having its seat in Dungarvan. Viking raiders first established a settlement at Waterford in 853. Waterford and all the other longphorts were vacated in 902, the Vikings having being driven out by the native Irish. The Vikings re-established themselves in Ireland at Waterford in 914 and built what would be Ireland's first city.

In 1137, Diarmuid MacMorrough, king of Leinster, failed in an attempt to take Waterford. He returned in 1170 with Norman mercenaries under Richard de Clare, 2nd Earl of Pembroke, who besieged and took Waterford. Throughout the medieval period, Waterford was Ireland's second city after Dublin. In the 15th century Waterford repelled two pretenders to the English throne: Lambert Simnel and Perkin Warbeck. As a result, King Henry VII gave the city its motto: Urbs Intacta Manet Waterfordia - Waterford remains the untaken city.

After the Reformation, Waterford remained a Catholic city and participated in the confederation of Kilkenny - an independent Catholic government from 1642-49. This was ended by Oliver Cromwell, who brought the country back firmly under British rule; his nephew Henry Ireton finally took Waterford in 1650 after the inhabitants surrendered.

The 18th century was a period of huge prosperity for Waterford. Most of the city's best architecture appeared during this time. In the 19th century, industries such as glass making and ship building thrived in the city.