Apart from the erection of a prison at Ferryquay Gate and the loss of some cannons 'lent' to the Parliamentary forces in 1650, the Walls lay virtually neglected for 40 years.
The deterioration that resulted in their weakened condition at the time of the Great Siege was noted by Lord Macaulay, the 19th century historian. His account was based on an inspection of the Derry fortifications by a French engineer, Jean Thomas. Lord Macaulay wrote:
And in truth, to a military eye, the defences of Londonderry appeared contemptible. The fortification consisted of a single wall overgrown with grass and weeds: there was no ditch even before the gates: the drawbridges had long been neglected: the chains were rusty and could scarcely be used: the parapets and towerswere builtafter a fashion which might well move [engineers] to laughter; and these feeble defences were on almost every side commanded by heights. Indeed those who laid out the city had never meant that it should be able to stand a regular siege, and had contented themselves with throwing up works sufficient to protect the inhabitants against a tumultuary attackof the Celtic peasantry.
There was great controversy over the Walls, mainly because they were not built in the normal pattern of that period. They lacked a moat, a counterscarp (the outer side of the ditch), buttresses, outworks and suitable platforms for the few cannons they had. But no-one could explain why, if the Walls were so badly constructed, the army of King James could not capture the city.
Whatever the reasons for the failure of the Great Siege, its cause was well known. The Protestant people of England were fearful of their Catholic king, James II, and replaced him. Prince William of the Netherlands, also a Protestant, was approached to lead a bloodless revolution in November 1688 which forced James to flee to France.

Captain Francis Nevill’s map of the besieged Derry in 1689.

In Ireland there was armed resistance amongst the Catholic Irish and English troops loyal to James. A contingent of these Jacobite forces (as they were known) arrived at Derry's Ferryquay Gate on 7 December 1688. Led by the Earl of Antrim, they had been sent by Tyrconnell, the Catholic viceroy, to take over command of the Derry garrison.
As the city's own troops had been sent to Dublin some weeks beforehand, the Protestant inhabitants feared a massacre. Thirteen apprentices of the city rushed to close the Gates and this action marked the symbolic beginning of the Great Siege. It is still celebrated today but on 18 December each year due to the change in calendar systems.
When Colonel Robert Lundy returned with the garrison's forces, he set about strengthening the Walls against a Jacobite attack. He ordered the building of a triangular defensive wall (a ravelin) outside Bishop's Gate and also outworks to Windmill Hill in the west and south to the west and south to the river.
On the eve of the siege, all the buildings outside the city Walls (on both sides of the Foyle) were set alight by the defenders to prevent them being used as cover by the besiegers.
On 18 April 1689 King James II arrived at Bishop's Gate in the mistaken belief that if he requested the garrison to surrender they would accede. His only reply was a barrage of shot which not only repulsed the Jacobites but registered the actual beginning of the siege. Four times King James demanded the surrender of the city. Four times he was refused. Frustrated, he returned to Dublin leaving his generals to besiege the Walls for 105 days.
During the siege the Walls were continuously bombarded by James's forces under Marshal Dc Rosen. Cannons and mortars caused great damage, mostly to the section between Bishop's Gate and Butcher's Gate which received the brunt of the attacks.
To reinforce the bulwarks the defenders made running repairs by using barrels filled with earth and gravel to replace the smashed parapets. At various times they had to place timber and sods outside against the Gates to protect them from the enemy's 'battering pieces'. They even built a small fort (from casks filled with clay) outside the Walls in the vicinity of Lord Docwra's Bulwark. It is called Walker's Fort in maps of the period, probably because the then joint Governor, Rev George Walker, ordered its construction.
By such makeshift means and by venturing outside occasionally to disrupt the enemy, the defenders contrived to defy the besiegers until relief came on 28 July 1689.
Dr William King, Bishop of Derry (1691-1702), said the siege failed because the besiegers were cowards. The supporters of King James argued it was the lack of cannons, mortars, scaling ladders and battering rams which made their task almost impossible.