During the Third Anglo-Dutch War, he drew up plans for the Zealand Expedition which was intended to land a newly formed English Army in the Netherlands.

In 1673 and 1674 he represented his country at the Congress of Cologne, and in the latter year he became Secretary of State for the Northern Department, having practically purchased this position from Arlington for £6,000, a sum that he required from his successor when he left office in 1679.

Just before his removal from the post of Secretary of State, he was arrested on a charge of being implicated in the Popish Plot,[5] but he was at once released by order of Charles II.

For this reason, the King, who was equally sceptical about the Plot's reality, wished to retain his services, at least in the short term.

Charles finally dismissed him after he gave orders to search Somerset House, the Queen's official residence, without the King's permission; the King, "in great anger" told him that "I marvel at your effrontery in searching my house... your head is turning.....I do not wish to be served by a man who fears anyone more than me".

More seriously in an age of marked class distinctions, it was considered improper that the sister of a Royal Duke should marry a country clergyman's son, and even her children are said to have objected to the marriage.

Williamson died at Cobham, Kent, on 3 October 1701, and was buried in Westminster Abbey, where his widow joined him a year later.

He had become very rich by taking advantage of the many opportunities of making money which his official position gave him; and despite the heavy debts left by her brother, his wife is also said to have brought him a fortune.

He has been described as one of the greatest English civil servants of his time, and is credited with building up an intelligence service as efficient as that which John Thurloe had operated under Oliver Cromwell.

On the other hand, his will, in which he remembered all those who had a claim on him, suggests that he did not lack a certain generosity of character; and he was capable of forming lifelong friendships, notably with Samuel Pepys.

Williamson also appears regularly in Andrew Taylor's series of novels about the adventures of Whitehall clerk James Marwood and architect Cat Lovett.