The castle consists of a two-storeyed main building protected by a curtain wall and towers, with a triangular gun platform projecting into the river.

The water flows slowly without strong currents and is free of rocks, while the surrounding hills provide shelter from the south-west wind.

These characteristics made the section of the river below Rochester Bridge a desirable anchorage for large ships, as they could be anchored safely and grounded for repairs.

[1] During Henry VIII's reign, the upper Medway gradually became the principal anchorage for ships of the Royal Navy while they were "in ordinary", or out of commission.

[2] Although the Thames had been defended from naval attack since Henry VIII's time, when five blockhouses were built as part of the Device Forts chain of coastal defences, there were no equivalents on the Medway.

Six "indifferent persons" chose a site opposite St Mary's Creek in Chatham, on 6 acres (2.4 ha) of land belonging to a Thomas Devinisshe of Frindsbury.

His deputy Humphrey Locke took the role of overseer, surveyor, and chief carpenter, while Richard Watts, the former Rochester mayor and victualler to the navy, managed the project on a day-to-day basis and handled the accounting.

[4] During the late 16th century, tensions grew between Protestant England and Catholic Spain, leading ultimately to the undeclared Anglo-Spanish War of 1585–1604.

The castle itself was poorly manned until Lord High Admiral Charles Howard, 1st Earl of Nottingham highlighted this and recommended that the garrison should be increased.

[5] Continued fears of a Spanish incursion led to the castle's defences being strengthened between 1599 and 1601 at the instigation of Sir John Leveson.

[11] Upnor Castle fell into Parliamentary hands without a fight when the English Civil War broke out in 1642, and was subsequently used to intern Royalist officers.

Parliamentary commander-in-chief Sir Thomas Fairfax inspected the castle and ordered further repairs and strengthening of the gun platforms.

The Dutch, under the nominal command of Lieutenant-Admiral Michiel de Ruyter, bombarded and captured the town of Sheerness, sailed up the Thames to Gravesend, then up the Medway to Chatham.

[12] The Dutch anchored in the Medway overnight on 12 June, while the Duke of Albemarle took charge of the defences and ordered the hasty construction of an eight-gun battery next to Upnor Castle, using guns taken from Chatham.

The castle's guns, the garrison's muskets, and the new battery were all used to bombard the Dutch ships when they attempted a second time to sail past Upnor to Chatham.

[12] The pro-government London Gazette reported that "they were so warmly entertained by Major Scot, who commanded there [at Upnor], and on the other side by Sir Edward Spragg, from the Battery at the Shoare, that after very much Dammage received by them in the shattering of their ships, in sinking severall of their Long Boats manned out by them, in the great number of their Men kill'd, and some Prisoners taken, they were at the last forced to retire.

"[14] Military historian Norman Longmate observes tartly, "in presenting damning facts in the most favourable light Charles [II's] ministers were unsurpassed.

"[12] Upnor Castle had been neglected previously, but the Dutch attack prompted the government to order that it be maintained "as a fort and place of strength".

New and more powerful forts were built farther down the Medway and on the Isle of Grain with the aim of preventing enemies reaching Chatham, thus making the castle redundant.

Upnor Castle ceased to be used as a storage magazine after 1827 and was converted into an Ordnance Laboratory (i.e. a workshop for filling explosive shells with gunpowder).

[17] The bombing dislodged pieces of plaster in the castle's south tower and gatehouse, under which were discovered old graffiti, including a drawing of a ship dated to around 1700.

[20] Upnor Castle's buildings were constructed from a combination of Kentish ragstone and ashlar blocks, plus red bricks and timber.

[21] A circular staircase within the building gives access to the castle's main gun platform or water bastion, a low triangular structure projecting into the river.

They were originally two-storeyed open-backed structures with gun platforms situated on their first floors, providing flanking fire down the line of the ditch around the castle's perimeter.

The two towers are linked to the main building by a crenellated curtain wall where additional cannon were emplaced in two embrasures on the north parapet and one on the south.

[25] The castle's principal buildings are situated on the east side of a rectangular courtyard within which stand two large Turkey oaks, said to have been grown from acorns brought from Crimea after the Crimean War.

[28] Between the magazines and the castle a Shifting House (for examining powder) had been built in 1811;[29] both it and an adjacent shell store of 1857 were likewise demolished in 1964.

They were constructed on top of earlier gun emplacements, of which earthwork traces can still be seen in the form of a broad bank running north-east from the castle towards the depot.

The Depot compound continued in Ministry of Defence hands until 2014, after which the area was due to be redeveloped as housing (with the surviving military buildings refurbished for light industrial use).