He started his career as private secretary to Henry Sidney, the Lord Deputy of Ireland, with whom he enjoyed a warm friendship and who employed him in numerous transactions of a highly confidential nature.
Like Sidney, Essex had great confidence in Waterhouse: on his deathbed, the Earl said a fond farewell to "Ned, my faithful friend".
This high opinion of his character was shared by nearly all the English administration in Ireland, and his great charm made him a favourite of Elizabeth I. Irish Catholics, on the other hand, have long remembered him as the man who tortured Dermot O'Hurley, the Archbishop of Cashel, by roasting his feet in the fire, in an unsuccessful attempt to make him renounce the Roman Catholic faith.
He played a major part in the negotiations for the cess, the much-resented tax for the upkeep of garrisons within the Pale, which was eventually abandoned due to the determined opposition of the Anglo-Irish gentry.
In the family chapel in Hertfordshire, he erected a memorial to his second wife Margaret, as a token of his "dear love" for that "worthy lady".