In 1646 General Preston established his chief quarters in the fortress, and in November of that year the Confederate Catholics halted in their march on Dublin between Leixlip and Lucan. They were commanded by Generals Preston and Owen Roe O’Neill. The King’s secretary and minister, Digby, was at Leixlip with Preston.

Plots and counter plots among the Confederate commanders made the once formidable army of no avail. Owen Roe, fearing some treachery, threw a wooden bridge across the Liffey, as a flood had destroyed the permanent one, and withdrew his forces into Meath.

Sir Nicholas Whyte recovered his lands of Leixlip by a Decree of Innocence. He died in 1654, and was buried at Leixlip.

Various historians have confused the fortress popularly called Leixlip Castle with a stronghold of less note designated the “Black Castle” of Leixlip, situated at the eastern end of the town. Although still known as the “Black Castle” this building has been so modernised that its original fortified structure is not noticeable.

That some discrepancies as to ownership existed in the written history of Leixlip Castle was first noted in 1901, but it was not until the following year that Lord Walter FitzGerald, in a note in the Journal of the Kildare Archæological Society, gave an extract from “The Civil Survey” of James Peisley and Henry Makepeace of 1654, in which the “Black Castle” of Leixlip is mentioned as belonging to the Earl of Kildare and “one ruined castle” to Sir Nycholas White, thus establishing the fact that there were two distinct castles at Leixlip owned by different persons.

The “Black Castle” is therefore no doubt the fortress alluded to in an inquisition held in September, 1612, which states that Gerald FitzGerald, son of Gerald, late Earl of Kildare, and uncle of Gerald, late Earl of Kildare, was seized of one castle, three messuages, one ruined water-mill, and forty acres of arable land at Leixlip. And again in 1621 the inquisition taken upon the death of Gerald, 15th Earl of Kildare, includes the Castle of Leixlip, &c. While the rental of the Earl of Kildare in 1657 mentions the black castle of Leixlip with sixty acres of land valued at £15 a year.

Leixlip Castle was purchased by the Right Hon. William Conolly, Speaker of the Irish House of Commons, at the beginning of the eighteenth century. He subsequently built the mansion of Castletown at Celbridge, but his nephew and heir occupied Leixlip Castle during the famine years of 1740 and 1741.

After this period the castle has been inhabited by many distinguished tenants.

It was a favourite residence of Primate Stone, and during Lord Townshend’s period of office he usually passed the summer there.

Many stories are told of this Viceroy’s fancy for mixing incognito with “all sorts and conditions of men.”