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The earl had five sons, one of whom became Henry Pierrepont, 1st Marquess of Dorchester, another was Francis Pierrepont (died 1659), a colonel in the parliamentary army and afterwards a member of the Long Parliament; and another was William Pierrepont (1608–1679), father-in-law of Gilbert Holles, 3rd Earl of Clare and also Henry Cavendish Duke of Newcastle upon Tyne.
He died unmarried at Dieppe in 1682 and was succeeded in the earldom by his brother William Pierrepont, 4th Earl of Kingston-upon-Hull.
A watercolour sketch titled 'In Captain Pierrepont's Grounds' was painted by Anthony Devis (1729–1817) not long after Captain William Pierrepont of HMS Naiad acquired Shalford Manor in 1800.