Wexford, Waterford and Duncannon
The New Model Army then marched south to secure the ports of Wexford, Waterford and Duncannon. Wexford was the scene of another infamous atrocity, when Parliamentarian troops broke into the town while negotiations for its surrender were ongoing, and sacked it, killing about 2000 soldiers and 1500 townspeople and burning much of the town. Cromwell's responsibility for the sack of Wexford is disputed. He did not order the attack on the town, and had been in the process of negotiating its surrender when his troops broke into the town. On the other hand, his critics point out that he made little effort to restrain his troops or to punish them afterwards for their conduct.
Arguably, the sack of Wexford was somewhat counter-productive for the Parliamentarians. The destruction of the town meant that the Parliamentarians could not use its port as a base for supplying their forces in Ireland. Secondly, the effects of the severe measures adopted at Drogheda and at Wexford were mixed. To some degree they may have been effective in discouraging future resistance.
The Royalist commander Ormonde thought that the terror of Cromwell's army had a paralysing effect on his forces. Towns like New Ross and Carlow subsequently surrendered on terms when besieged by Cromwell's forces. On the other hand, the massacres of the defenders of Drogheda and Wexford prolonged resistance elsewhere, as they convinced many Irish Catholics that they would be killed even if they surrendered.
Such towns as Waterford, Duncannon, Clonmel, Limerick and Galway only surrendered after determined resistance. Cromwell was unable to take Waterford or Duncannon and the New Model Army had to retire to winter quarters, where many of its men died of disease—especially typhoid and dysentery. (The port towns of Waterford and Duncannon eventually surrendered after prolonged sieges in 1650.)
Read more about this topic: Cromwellian Conquest Of Ireland