He was born at Bala, Merionethshire, in 1637, son of Edward Lloyd, a clerk there. After spending two years at Ruthin School, he was admitted, on 23 February 1655, sizar at St. John's College, Cambridge, graduated B.A. and M.A., and was in 1670 created D.D. by royal letters. For some time, shortly after taking his master's degree, he was chaplain to the English Merchants' Factory in Portugal, and vicar of Battersea, Surrey. He was Archdeacon of Merioneth from 1668 to 1672. He subsequently became chaplain to Thomas Clifford, 1st Baron Clifford of Chudleigh and was prebendary of Caddington Minor in St Paul's Cathedral from 4 May 1672 to March 1676. On 6 April 1675 he was elected bishop of Landaff, in succession to Francis Davies. He was transferred, 10 April 1679, to Peterborough, and on 11 June 1685 to Norwich. He wanted to sign the petition for which the Seven Bishops were tried in 1688, but his letter was delayed; he helped them in preparing their defence, which led to a threat that he should yet 'keep company with them'. At the Glorious Revolution Lloyd, although attending one meeting of the Convention parliament, did not come in to take the oaths by the date fixed. He subsequently absolutely declined to take them, but remained in the possession of his preferments until 1 August 1690, when he was suspended from the performance of his ecclesiastical functions until 1 February. 1691. He then was formally deprived. In 1692 William Sancroft, the deprived archbishop, formally delegated to Lloyd, as his proxy, the exercise of his archiepiscopal powers in spiritual matters. Lloyd signed two published letters, one A Vindication of the Bishops, 1690, and another appealing to all Christian people for assistance to the suffering nonjuring clergy, July 1695. When a list of the nonjuring clergy was taken over to James II at the Château de Saint-Germain-en-Laye, the exiled king directed Sancroft and Lloyd each to nominate one of the suspended clergymen for the episcopate. Lloyd nominated Thomas Wagstaffe as suffragan bishop of Ipswich, and performed the consecration 24 February 1693 in a private house, assisted by the deprived bishops of Peterborough and Ely. Lloyd retired to Hammersmith, where he continued though with caution to exercise his episcopal functions. He died 1 January 1710, and was buried in the belfry of Hammersmith parish church, in accordance with his own wish. He had outlived all the deprived bishops except Thomas Ken. His death was followed by the return of Henry Dodwell, Robert Nelson, Brokesby and others to the national church, Ken having expressly declared his wish that the schism should be ended.
Family
He left a widow, Hannah, and a son John, who died in 1706, a fortnight after he had married a daughter of Dr Humphrey Humphreys.