Late in 1641, Protestant refugees, displaced by the insurgents, began to arrive in the town, creating tension among the Catholic townspeople.

In 1645 Confederate troops under Thomas Preston besieged and captured nearby Duncannon from its English garrison, thus removing the threat to shipping coming to and from Waterford.

The Confederates finally agreed a treaty with Charles I of England in 1648, in order to join forces with the Royalists against their common enemy, the English Parliament, which was both anti-Catholic and hostile to the King.

This fear was accentuated by the fate of Drogheda and nearby Wexford which had recently been taken and sacked by Cromwell's forces and their garrisons massacred.

Its port allowed for the importation of arms and supplies from continental Europe and its geographical position commanded the entrance of the rivers Suir and Barrow.

Before besieging Waterford, Oliver Cromwell had to take the surrounding garrisons held by Royalist and Confederate troops in order to secure his lines of communication and supply.

A counter-attack on Carrick by Irish troops from Ulster under Major Geoghegan was repulsed on 24 November, leaving 500 of the Ulstermen dead.

However, Waterford still had access to reinforcements from the west and up to 3000 Irish soldiers (from the Confederate's Ulster Army) under Richard Farrell were fed into the city in the course of a week.

Farrell, having been a successful officer in the Spanish army, was highly trained and experienced in siege warfare from battles in Flanders.

The capture of a fort at Passage East enabled him to bring up siege guns by sea, but the wet weather meant that it was all but impossible to transport them close enough to Waterford's walls to use them.

His troops were allowed to march away to Galway or Athlone, which were still in Irish Catholic hands, but he surrendered all the artillery, ammunition and ships in Waterford.