[3] Strengthened by Sir James Hamilton of Finnart in the mid-16th century, the castle became one of the most advanced artillery fortifications of its time in Scotland.

[4] The barony of Blackness was held in the mid-15th century by Sir George Crichton, Lord High Admiral of Scotland, Sheriff of Linlithgow, and later Earl of Caithness.

His dispossessed heir, James Crichton, captured the castle and held it briefly against the King, who besieged and recaptured it the same year.

[5] Blackness became a royal fortress, as well as continuing to serve as a prison, and was put into the care of a keeper, who was often the Sheriff of Linlithgow.

Having spent time in Europe studying the subject, he designed his own castle at Craignethan in Lanarkshire as a showcase for his ideas.

[10] At Blackness, he introduced technological innovations including a complex entrance with a caponier, one of only three surviving in Scotland (the others being at Craignethan and Stirling Castle).

[11] Work continued after Finnart's execution for treason in 1540, under the superintendence of the parson of Dysart,[9] and the "dungeon" and kitchen towers were roofed with turf called "brume and dovet".

[12] Major building works came to a halt in 1542 on the death of James V. Following the battle of Pinkie, on 15 September 1547 Richard Broke and the Galley Subtle rowed up the river to Blackness.

[13] During the crisis of the Scottish Reformation the castle was surrendered by negotiation to James Hamilton, Duke of Châtellerault as leader of the Lords of the Congregation.

During the Marian civil war which followed the forced abdication of Mary, Queen of Scots in 1567, the garrison of Blackness remained loyal to her.

[17] The castle's defences were not tested again until 1650, when Oliver Cromwell's New Model Army besieged Blackness during his invasion of Scotland.

However, by this time artillery technology had improved beyond anything that Finnart's defences could withstand, and the garrison soon surrendered under bombardment from land and sea.

[18] The castle was not repaired until 1667, when it was again used as a prison, holding a number of Covenanters; religious rebels who opposed the King's interference in church affairs.

Further changes were made in 1693, when the spur was heightened with a wall-walk, and the north tower was reduced to provide three gun platforms overlooking the Forth.

[20] After the Union of Scotland and England in 1707, the castle ceased to be a prison,[18] instead being one of four Scottish fortresses to be maintained and garrisoned by the British Army, the others being Stirling, Dumbarton and Edinburgh.

The castle is said in popular legend to have a ley tunnel linking it with the House of the Binns, which lies about two miles (three kilometres) south.

The tower is built over the thick-walled artillery positions in the basement, which defend the south and east approaches, and have similarities with the contemporary "blockhouse" at Dunbar Castle, further along the coast.

[18] The South Tower provided the main accommodation in the castle, with chambers in the north-west wing, and a large hall on the upper storey.

Men such as Cardinal Beaton, Archbishop of St Andrews and James V's ambassador to France, and Archibald Douglas, 6th Earl of Angus, regent of Scotland in the 1520s, would have had a reasonably high standard of living, including their own servants, while in prison.

The 16th-century forework, or "spur", which provides additional protection for the main gate, is largely the work of Sir James Hamilton of Finnart, and contains numerous defensive features.