Before 1641 he married his kinswoman, Mary Nugent (widow of Christopher Plunkett, who was a younger son of Christopher Plunkett, 8th Baron of Dunsany), and daughter of Sir Thomas Nugent, 1st Baronet of Moyrath and his wife Alison Barnewall, daughter of Robert Barnewall of Robertstown, County Meath.
While attempting to make his way back to Ireland in December 1641 upon the outbreak of the 1641 Rebellion, Nugent was arrested on suspicion of complicity in the uprising. He subsequently served as cavalry commander during the Irish Confederate Wars, seeing action at the Battle of Dungan's Hill in August 1647, where he was captured. He later served as General of the Forces of Leinster from 1650 to 1652. His conduct as a military leader was severely criticised by his own side: he was called a general who had never put an army in the field, nor gained the support of anyone who could perform an action worth sixpence. During Oliver Cromwell's campaign in Ireland, Clonyn Castle, the main Nugent residence, was burnt: according to one account Lord Westmeath burnt it himself to prevent it falling into his enemy's hands. He submitted to the Parliamentary forces in the latter year but was excluded from the Act of Settlement 1652 and transplanted to Connaught, despite his rather abject pleas to be allowed to remain, and protestations of loyalty to the new regime. After the Restoration of Charles II, he received a large pension as a reward for his loyalty to the Crown, which, in accordance with the general policy of Indemnity and Oblivion, was prepared to overlook his later subservience to Cromwell. He took no further part in public affairs.
Lady Alison Nugent, married Henry Dowdall of Brownstown, County Meath
Lady Jane Nugent, married Brigadier-General Alexander MacDonnell of County Leitrim in 1685.
He was succeeded by his grandson, Richard Nugent, 3rd Earl of Westmeath, eldest son of Christopher, Lord Delvin. The third Earl was a monk who spent most of his adult life in France, and on his death, the title passed to his two younger brothers, Thomas and John, in turn.