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 (ib. 1671, p. 238), he obtained permission to go to Ireland for six months, arriving at Kinsale on the 27th. He was recalled to London in September by his appointment as envoy extraordinary to Brussels. A warrant was issued on 19 Oct. to pay him 4l. per diem and 300l. for his equipage, and, having received his instructions on the 25th, he set out from London on the 31st. After his return, early apparently in the year following, he refrained from meddling personally in the political intrigues of the time, though from his correspondence it would seem that he deplored Charles's conduct in the matter of the declaration of indulgence, inclining generally to Sir William Temple's view of the situation. He was M.P. for Penryn in 1673, and for Lostwithiel in 1685. On 6 Aug. 1677 the university of Oxford conferred the degree of D.C.L. on him, and in 1679 he purchased from Sir Humphrey Hooke the manor of King's Weston in Gloucestershire, where he entertained King William on his return from Ireland in 1690. Having resigned his place as a clerk to the privy council on 5 Dec. 1679, he was in the spring of the following year (1680) sent as envoy extraordinary to the elector of Brandenburg, in pursuance of Temple's plan of creating a defensive alliance against France. On his way he communicated his instructions to the Prince of Orange, and afterwards entered into negotiations with the courts of Brunswick-Lüneburg, then rising into importance in consequence of the death of the Duke of Hanover. But perceiving shortly after his return that a reaction was setting in against the whigs, he retired to his seat at King's Weston (cf., Life of Petty, p. 246).

On 1 Dec. 1680 he obtained a reduction of the quit-rents imposed on his Irish estates by the Acts of Settlement, and on 10 Feb. following conveyed to the crown, for the sum of 1,041l. 2s. 6d., that part of the lands of Ringcurran occupied by the fort. In 1682 he founded and endowed an almshouse for eight helpless men and women on his estate of Dromderrick, within the liberties of Kinsale, being led, as he says himself, to this act of charity by a lively remembrance of the sufferings he had undergone during his travels abroad ‘for want of such conveniences,’ being in his youth of a sickly and delicate nature. He continued to live in retirement at King's Weston till the accession of William III, amusing himself with his garden, and profiting by the horticultural knowledge of his friend John Evelyn.

At the revolution he was made a commissioner for managing the customs on 19 April 1689. He accompanied William to Ireland in the following year, and was by him appointed principal secretary of state for that kingdom, holding the office till his death. Shortly after his appointment Swift, bearing a letter of introduction from Sir William Temple, unsuccessfully solicited the post of amanuensis to him (, Life of Swift, p. 27; Lives of the Poets, 1854, iii. 160). On 1 Dec. 1690 he was elected president of the Royal Society, holding that office for five successive years (, Royal Society; cf., Diary, ii. 310). On 12 June 1697 he was superseded by Sir J. Austen as commissioner of customs, and on 11 July of the following year, being clerk of the crown and prothonotary of the court of king's bench, he surrendered the same to the king, who on 23 Sept. regranted it to his son Edward, in reversion after the determination of the patent granted to Philip Savage and Richard Ryves, which being surrendered on 14 Aug. 1713, the same was conferred on Edward and his son for life.

Southwell died at King's Weston on 11 Sept. 1702, and was buried in Henbury church, Gloucestershire, beside his wife, who predeceased him, on 13 Jan. 1681–2, under a monument with an elaborate inscription. He married, 26 Jan. 1664, Elizabeth, eldest daughter of Sir Edward Dering of Surrenden-Dering in Kent, ‘a very pretty woman’ according to Pepys, and by her had issue: Rupert born on 21 May 1670, and died on 8 May 1678: Edward, his heir (see below); and four daughters—Helena, Elizabeth, Mary, and Catherine. According to Evelyn, he was ‘a sober, wise, and virtuous gentleman,’ and, it may be added, an industrious official. His portrait, painted by Kneller, belongs to the Royal Society. It was engraved by J. Smith in 1704 (cf., p. 175). He was also a man of some literary acquirements and began a life of James, first duke of Ormonde, which his age and infirmities prevented him from finishing. The manuscript, ‘consisting of about one hundred pages in folio, and containing such domestic information touching the duke's life as he had received from his grace's own mouth,’ was lent by his son Edward to Thomas Carte. Apart from his official and private correspondence, noted below, attention may be especially directed to his ‘Reflections on the Irish Rebellion’ (Addit. MS. 21129); ‘Remarks on Mazarin's Negotiations for the Treaty of the Pyreenes’ (Addit. MS. 20722); and ‘Rights and Jurisdiction of the Lord High Admiral of England asserted in Ireland, laid before the Admiralty by Sir Robert Southwell, Vice-admiral of Munster,’ 1693 (Egerton MS. 744).