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 of Whitechurch, Buckinghamshire, and Margaret, daughter of Henry Turner of Blunt's Hall in Suffolk, was born at Helmstedbury, Hertfordshire, in 1535. His father was sometime auditor to Henry VIII, and a family tradition relates that the king, one day visiting him, ‘gave a Benjamin's portion of dignation to this Edward, foretelling by his royal augury that he would be the crown of them all, and a man of great honour and wisdom, fit for the service of princes.’ When twelve years old Waterhouse was sent to Oxford, ‘where for some years he glistered in the oratorick and poetick sphere, until he addicted himself to conversation and observance of state affairs.’ Going to court, he found a patron in Sir Henry Sidney [q. v.], and when the latter was in 1565 appointed lord deputy of Ireland, Waterhouse accompanied him thither in the capacity of private secretary. He was made clerk of the castle chamber on 1 Feb. 1566, and about the same time received a grant of a lease of the manor of Evan in co. Kildare, together with the corn tithes of Dunboyne in co. Meath. He was devotedly attached to Sir Henry Sidney, by whom he was employed in services of a very confidential nature. He accompanied the lord deputy on his tour through the island in 1568, and, being left by him to look after Carrickfergus, he was instrumental in obtaining a charter for that town in 1570; he was in consequence created a freeman, and nominated to represent it in any parliament subsequently to be held, which he accordingly did in 1585. Waterhouse surrendered his office of clerk of the castle chamber in October 1569, and when Walter Devereux, first earl of Essex [q. v.], in 1573, embarked in a scheme for the plantation of co. Antrim, he induced Waterhouse to enter his service. He was employed by the earl in frequent missions to England connected with the sale of his property and furnishing provisions for his undertaking, and by his discretion and devotion won that unfortunate nobleman's gratitude. He attended him in his illness, and it was in his arms that the earl breathed his last, saying, ‘Oh, my Ned! oh, my Ned! Thou art the faithfullest and friendliest gentleman that ever I knew.’ Being by the failure of Essex's enterprise deprived of employment, he obtained a grant on 25 June 1576 of a pension of 10s. English a day, which was subsequently, on 26 June 1579, confirmed to him for life. He was appointed secretary of state by Sir Henry Sidney, and in 1576–9 was several times sent to England to bring over treasure and in connection with the question of cess. He was added to the commission to inquire into concealed and forfeited lands in 1578. On 5 Feb. 1579 he obtained a grant of the collectorship of customs on wine in Ireland; on 27 June he was appointed commissioner for check of the army; on 7 July receiver-general in the exchequer, and on 25th of the same month receiver of all casualties and casual profits falling to the crown. He attended the movements of the army under Sir William Drury [q. v.] in Munster from August to November that year, during the rebellion of James Fitzmaurice and Sir John Desmond, adding to his other duties that of overseeing the victualling department. Towards the latter end of October he was sworn a privy councillor; but the outbreak of the rebellion of the Earl of Desmond in November recalling him to his post with the army in Munster, his time was fully occupied for the two following years in discharging his duties as secretary, commissioner for check of the army, and overseer of the commissariat. On 17 June 1580 he obtained a grant of the office of overseer and water bailiff of the Shannon, with valuable perquisites; on 10 April 1581 he was appointed a commissioner for ecclesiastical causes, and on 22 July was granted a lease for twenty-one years of the lands of Hilltown in Meath. As he had served Essex and Sidney in all fidelity, so he served Arthur, lord Grey de Wilton, and Sir John Perrot, living at peace with all men, and all men having at one time or another a good word for him. Despite his ‘weak body,’ he was assiduous in the discharge of his numerous offices, and on 13 Jan. 1582 reported that he had collected in bonds and recognisances casualties to the amount of 100,000l. On 26 Aug. that year he obtained a grant of the castle and lands of Doonass in co. Clare, to be held in fealty, only rendering to the deputy one pair of gloves whenever he visited the castle. The rewards, more numerous than valuable, heaped upon him aroused Elizabeth's jealousy, especially that of water bailiff of the Shannon and custodian of the boats at Athlone, and in the autumn he was ordered over to England. His modest behaviour and the warm credentials he brought from Ireland won Burghley's favour, while his offer to surrender his obnoxious patent of water bailiff mollified Elizabeth, though she insisted on having a list made out of all patents, fees, &c. granted to him during the last seven years.

Returning to Ireland in April 1583, Waterhouse had in the following March the disagreeable task imposed upon him, along with Sir Geoffrey Fenton, of torturing Dermot O'Hurley [q. v.], titular archbishop