Royal Fleet

The Royal Fleet is the naval force directly commanded by the King of the Andals and the First Men. It consists of a large number of ships based at King's Landing and Dragonstone. It falls under the command of the Master of Ships, one of the members of the king's Small Council.

During the reign of King Robert Baratheon, his Master of Ships was his younger brother Stannis.

During the War of the Five Kings, the fleet becomes divided between the forces of Joffrey Baratheon and Stannis. When their two forces clashed at the Battle of the Blackwater, losses to the old "Royal Fleet" were bound to be high, as its ships were fighting each other, and in the resulting battle the old "Royal Fleet" was devastated. Stannis lost almost all of his ships, and was forced to withdraw on a few auxiliary sellsail ships that he had hired. The smaller number of ships that Joffrey controlled faired only slightly better, as Tyrion gave no more than token resistance before springing his wildfire trap.

Season 2
As Stannis Baratheon was his brother Robert's Master of Ships, when the War of the Five Kings breaks out upon Robert's death, a disproportionately large portion of the Royal Fleet (primarily based at Dragonstone) joins Stannis' faction when he declares himself king. This then becomes "his" Royal Fleet. However, Stannis has a very small land army and only has the allegiance of a few Houses from the Crownlands holding islands in the Narrow Sea. Thus Stannis' dominance at sea is one of his few advantages at the outset of the war. Stannis then augments the Royal Fleet by recruiting an additional thirty warships belonging to sellsail and pirate Salladhor Saan.

Matthos Seaworth and his father debate the nomenclature of what to call "the Royal Fleet" where there are several kings in the realm. Later, when Stannis's forces approach King's Landing, King Joffrey Baratheon expects the twenty warships of the Royal Fleet squadron based at King's Landing to sail out to meet them. However, Tyrion Lannister, Acting Hand of the King, has ordered the Royal Fleet to fall back so as not to be destroyed by Stannis's numerically superior forces. Instead he commits a single ship packed with wildfire to the attack and has Bronn detonate the vessel when it has passed through the leading elements of Stannis's fleet. The resulting explosion destroys a large portion of Stannis's fleet and kills thousands of men. It is the opening move of the Battle of the Blackwater. Tyrion's move ensures that nineteen warships of the Royal Fleet survive the battle.

In the books
According to semi-canon material approved by George R.R. Martin, the Royal Fleet consists of 210 warships, at least 80 of which are full warships dipping 100 oars or more. The Royal Fleet's flagship is the King Robert's Hammer, which dips 400 oars and is the largest warship in Westeros. The Royal Fleet is divided into two squadrons, a smaller one of 50 based at King's Landing and a larger force of around 160 ships based at Dragonstone. The position of Dragonstone and the size of the fleet there makes an attack on King's Landing by sea almost impossible to mount for any foreign power.

In the A Song of Ice and Fire novels, when the War of the Five Kings breaks out, Stannis Baratheon seizes control of the ships at Dragonstone and uses them in his attack on King's Landing. Most of the Royal Fleet's crews and captains stay loyal to Stannis because he had been commanding them as Master of Ships during his brother Robert's entire reign, even leading them into a decisive naval victory at the Battle of Fair Isle during the Greyjoy Rebellion. Unlike in the TV series, the Royal Fleet does participate in the Battle of the Blackwater in the books. The fleet engages Stannis's force and draws them into the mouth of the Blackwater Rush. Tyrion raises a massive chain to trap the fleet in the river and detonates barrels of wildfire hidden on the floor of the river and inside several of the royal ships. This move destroys most of Stannis's fleet, but also more than half of Joffrey's fleet. Stannis was forced to retreat on the sellsail ships of Salladhor Saan, which survived the wildfire because Ser Imry Florent contemptuously insisted that they only follow behind the main fleet as a rearguard.

By the conclusion of the battle, the old "Royal Fleet" has been functionally destroyed, with only about a dozen ships loyal to Joffrey still afloat in King's Landing. Another dozen or so survived but were severely damaged and forced into dock for repairs - such as the royal flagship King Robert's Hammer. Worse, the King's Landing dockyards were also destroyed in the blaze, forcing the damaged ships to limp up the coast to Duskendale for repairs, making the situation even more desperate. The rest of the Royal Fleet had been obliterated by the wildfire - including the Queen Cersei. All of Stannis' ships are destroyed, forcing him to rely on the thirty Lyseni sellsail ships of Salladhor Saan to retreat his few remaining men (under 2,000) to Dragonstone. Four or so ships were so far upriver that they managed to escape the wildfire, but were then trapped with the city guarding the river's mouth, so their crews decided to sink them rather than let them fall into Lannister hands (two remained active making piratical attacks on river shipping, but they were still trapped on the river with their capture inevitable).

Up until the Battle of the Blackwater, no faction (other than the ironborn) made extensive use of ships to maneuver in the war. Stannis was gathering his ships for a quick and decisive strike at King's Landing itself, while the Lannisters were holding their ships back to brace for Stannis' assault. While the Battle of the Blackwater did remove the threat of further assaults on the capital by Stannis, this left Joffrey's Royal Fleet so depleted that no thought was given to naval maneuvers against other factions such as House Stark (i.e. with barely a dozen ships afloat, the Lannisters never considered making a sea-based invasion of White Harbor in the North). Thus the War of the Five Kings would continue to be decided by land forces.

The naval forces available to the Iron Throne were so depleted that for many months after the battle no thought was given to making a follow-up assault upon Stannis' stronghold on Dragonstone island, because the Lannisters simply no longer possessed the number of ships needed to mount an invasion of the formidable island fortress. Stannis was left sidelined from the war, bereft of most of his army and unable to make any significant strikes again, while the Lannisters were content to let him rot on Dragonstone while they rebuilt their superior forces (as seen in Season 3 of the TV series).

The Royal Fleet is one of the few major fleets operated by Westerosi forces. Many major lords of coastal areas will keep a warship or three on hand for fighting pirates, but there are only a few large-scale fleets besides the Royal Fleet itself. The ironborn maintain many hundreds of longships, including the formidable Iron Fleet, which consists of almost all of the ironborn's larger warships and galleys. House Redwyne also commands a substantial fleet based at the Arbor. House Lannister maintains a small coastal fleet at Lannisport, burned during the Greyjoy Rebellion but subsequently rebuilt. House Stark has had no strength at sea since Brandon the Burner destroyed the Northern fleet, after his father sailed west into the Sunset Sea and never returned.

At the outbreak of the War of the Five Kings, the Royal Fleet in the east consists of about 200 war galleys plus support ships, and the Redwyne Fleet also consists of about 200 war galleys plus support ships. The Iron Fleet consists of 100 longships, which are faster than war galleys but have less tonnage, but are only the core ships which are held to belong to the Iron Islands as a whole, directly under the command of House Greyjoy, and which can dip 100 oars each. The Iron Fleet is supported by other longships which belong to each of the noble Houses of the ironborn, which collectively number over 500 longships, though most dip only 20 oars and are meant to quickly transport raiding parties, not to engage in pitched ship-to-ship naval combat. Other major lords might keep a war galley or three in their ports to ward off pirates, but do not possess major offensive capabilities. While House Lannister can afford a reasonably sized fleet, due to the close proximity of the Iron Islands to the coasts of the Westerlands their ships are kept in a defensive posture to protect ports such as Lannisport from attack: this ties down House Lannister's personal naval assets during the war.

The Royal Fleet is left crippled after the Battle of the Blackwater, reduced to barely a tenth its former size (and even that is being generous, as half of the surviving ships are crippled and laid up in drydock). Given that the ironborn have seceded from the realm and taken the Iron Fleet with them, and the Royal Fleet was functionally destroyed at the Battle of the Blackwater, this leaves the Redwyne Fleet as the one remaining significant naval force under the Iron Throne's control. This results in the Lannisters becoming even more dependent on the Tyrells, much to Cersei's consternation, as the Iron Throne must now rely on the Tyrells and their Redwyne vassals as their main naval force.