Full control of the town was not secured until Duncannon Fort across Waterford Harbour was also taken from its garrison under Michael Burke shortly afterwards.

In both cases the garrisons were allowed to march out under escort to Jacobite-held Mallow in County Cork, but were denied the "honours of war" which they demanded.

Although preparations had been made to resist a siege, including the destruction of outlying suburbs which might offer cover to the attackers, the appearance of Kirke's forces shook Barret's confidence and he immediately opened negotiations to turn over the town in exchange for being able to take his 1,400 men westwards to rejoin the Jacobite army.

However, when a Royal Navy squadron under Cloudesley Shovell sailed into Waterford Bay, Burke changed his mind and surrendered on condition that his men could march out for Jacobite territory, rather than being held as prisoners.

[3] Some of the Catholic population of the area took advantage of William's Declaration of Finglas which had offered a pardon to Jacobite supporters while others left with the departing troops.