The arguments over the maintenance of the castle and blockhouses continued in early 1600s.
The town of Hull argued that since the revenues of £50 granted in 1553 were insufficient to maintain these defences, they should be allowed to use royal customs duties to assist in the work, particularly in protecting the east bank of the river from erosion.
As a result, another court case was brought by the Crown in 1601.
A commission was established to examine the defences and concluded that the position of the castle meant that it was militarily useless, and as a consequence it had not been garrisoned or maintained for many years, resulting in it falling into total disrepair.
The commission's report led to the town carrying repairs to the earthwork defences over the coming year.
The Crown dropped its law case, but a third case was brought in 1634, only to see the Crown pull out of the proceedings once again.
By now, the corporation argued it had spent £11,367 on the defences.

Around 1627, Robert Morton, the mayor of Hull, had an additional rectangular earthwork battery of four guns constructed around the south blockhouse to defend the estuary against a potential Spanish and French invasion threat.
The South End Fort was built on the other side of the river from the South Blockhouse at the same time, provided supporting crossfire.
In 1634, a survey showed the North Blockhouse to be mounting 24 pieces of artillery, the castle 29, and the South Blockhouse 24 guns.
Catholic recusants continued to be detained in the castle and blockhouses, where they were ill-treated by the keepers, typically men with strong Puritan sympathies.

At the outbreak of the English Civil War in 1642, Hull sided with Parliament against King Charles I. Hull was besieged by the Royalists in July 1642, and the South Blockhouse may have been used to drive off a Royalist naval vessel approaching the estuary.
In 1643, the mayor, Thomas Raikes, and the Parliamentarians in Hull concluded that the governor, Sir John Hotham, was planning to seize the castle and the wider town for the King.
In a pre-emptive strike in June, Captain Moyer landed 100 troops from the Parliamentary warship the Hercules and took the castle and blockhouses, while Raikes seized the town itself.
Hotham was later executed.
A further siege followed in 1643, during which the area to the east of the castle and blockhouses was deliberately flooded by the defenders to provide additional protection.
In September, the south bastion of the North Blockhouse was accidentally blown up by one of the defenders, killing five men.

The artillery exchanges during the sieges and the activities of the garrisons had caused considerable damage, and at the end of the conflict the military Governor of Hull ordered repairs.
The North Blockhouse needed work costing £1,500, Hull Castle, £300, and the South Blockhouse, £220.
During the interregnum, the fortifications were maintained, despite complaints from the town at the costs, and were used to hold both prisoners of war and political prisoners.
Henry Slingsby, for example, was held at the castle before his trial in London.

When Charles II was restored to the throne in 1660, the interregnum army was demobilised; a guard-force remained in Hull to protect the arsenal there, being officially referred to as the "Hull Blockhouse" garrison.
All three sites were garrisoned: surveys reported that the South Blockhouse was in a good condition and held 21 guns, the castle was in a poor condition and held only 8 light guns, and the North Blockhouse was in a "ruinous" condition and held 10 guns.
An order was taken to strip the most ruined parts of the North Blockhouse of its timber, bricks and lead to help improve the remainder, supplemented by additional supplies of timber and bricks donated by the Crown, but the material was misappropriated and used, in part, for construction work on the houses of the Governor and his deputy.

The defences were neglected for several decades, despite calls for improvements and when the military engineer Sir Martin Beckman visited the sites in 16
The arguments over the maintenance of the castle and blockhouses continued in early 1600s. The town of Hull argued that since the revenues of £50 granted in 1553 were insufficient to maintain these defences, they should be allowed to use royal customs duties to assist in the work, particularly in protecting the east bank of the river from erosion. As a result, another court case was brought by the Crown in 1601. A commission was established to examine the defences and concluded that the position of the castle meant that it was militarily useless, and as a consequence it had not been garrisoned or maintained for many years, resulting in it falling into total disrepair. The commission's report led to the town carrying repairs to the earthwork defences over the coming year. The Crown dropped its law case, but a third case was brought in 1634, only to see the Crown pull out of the proceedings once again. By now, the corporation argued it had spent £11,367 on the defences. 
Around 1627, Robert Morton, the mayor of Hull, had an additional rectangular earthwork battery of four guns constructed around the south blockhouse to defend the estuary against a potential Spanish and French invasion threat. The South End Fort was built on the other side of the river from the South Blockhouse at the same time, provided supporting crossfire. In 1634, a survey showed the North Blockhouse to be mounting 24 pieces of artillery, the castle 29, and the South Blockhouse 24 guns. Catholic recusants continued to be detained in the castle and blockhouses, where they were ill-treated by the keepers, typically men with strong Puritan sympathies.
At the outbreak of the English Civil War in 1642, Hull sided with Parliament against King Charles I. Hull was besieged by the Royalists in July 1642, and the South Blockhouse may have been used to drive off a Royalist naval vessel approaching the estuary. In 1643, the mayor, Thomas Raikes, and the Parliamentarians in Hull concluded that the governor, Sir John Hotham, was planning to seize the castle and the wider town for the King. In a pre-emptive strike in June, Captain Moyer landed 100 troops from the Parliamentary warship the Hercules and took the castle and blockhouses, while Raikes seized the town itself. Hotham was later executed. A further siege followed in 1643, during which the area to the east of the castle and blockhouses was deliberately flooded by the defenders to provide additional protection. In September, the south bastion of the North Blockhouse was accidentally blown up by one of the defenders, killing five men. 
The artillery exchanges during the sieges and the activities of the garrisons had caused considerable damage, and at the end of the conflict the military Governor of Hull ordered repairs. The North Blockhouse needed work costing £1,500, Hull Castle, £300, and the South Blockhouse, £220. During the interregnum, the fortifications were maintained, despite complaints from the town at the costs, and were used to hold both prisoners of war and political prisoners. Henry Slingsby, for example, was held at the castle before his trial in London. 
When Charles II was restored to the throne in 1660, the interregnum army was demobilised; a guard-force remained in Hull to protect the arsenal there, being officially referred to as the "Hull Blockhouse" garrison. All three sites were garrisoned: surveys reported that the South Blockhouse was in a good condition and held 21 guns, the castle was in a poor condition and held only 8 light guns, and the North Blockhouse was in a "ruinous" condition and held 10 guns. An order was taken to strip the most ruined parts of the North Blockhouse of its timber, bricks and lead to help improve the remainder, supplemented by additional supplies of timber and bricks donated by the Crown, but the material was misappropriated and used, in part, for construction work on the houses of the Governor and his deputy. 
The defences were neglected for several decades, despite calls for improvements and when the military engineer Sir Martin Beckman visited the sites in 16
Hull Castle