James Stuart, Duke of York, was Lord High Admiral from 1660 to 1673 and had taken a close personal interest in the Navy. But he was required to step down from this post in 1673 after the passing of the Test Act. Interestingly, he remained Lord High Admiral of Ireland and of the Plantations, which allowed him a share of profits from prizes and wrecks in those jurisdictions. He had also, shortly before his resignation in England, managed to succeed to the same responsibility for Scotland. The previous holder of the post, a distant Stuart cousin, drowned in the icy waters off Copenhagen while attempting to get on board his own ship - having enjoyed rather too much Danish hospitality. (Davies 2017, p. 108)

For the next six years (1673 - 1679), James continued to play a considerable role behind the scenes while the Admiralty was technically in commission (overseen by a committee). The First Lord (chairman) was Prince Rupert Wittelsbach, the king's cousin, but he was not setting policy. The king and his brother took personal charge of running the navy. Following the exclusion crisis and something of a revolt by Rupert, new commissioners were appointed. Many were long-term critics of naval administration, but without experience of managing affairs themselves.

Charles Stuart continued to interfere in decisions and in 1684 dissolved the commission of the Admiralty to take formal control, while in reality permitting James to act as if he were Lord High Admiral again (J sailed into Spithead flying the admiral's flag in 1684, p.122).

Naval officers were often seen at court - sometimes, indeed, when they were meant to be at sea. Charles and James liked having naval men around them.

As well as being permitted such generous access, sea-officers benefitted from royal patronage in a number of other ways. During the second Anglo-Dutch war in particular, successful officers were often granted prize ships, which could either be sold or set out as privateers or merchantmen. During peacetime, favoured captains were granted 'good voyages', usually within or from the Mediterranean, which enabled them to carry merchants bullion and charge a commission for so doing. Above all, sea-officers were often honoured with knighthoods, sometimes as a sort of 'lifetime achievement award', more often as a reward for notable service in action. The honour was bestowed on men from relatively humble backgrounds, at once catapulting them into the ranks of the armigerous gentry. Richard Munden, knighted in 1673 for capturing St Helena from the Dutch, was a son of the ferryman at Chelsea; John Wetwang, a veteran captain who was knighted in 1680, came from Northumberland freeholder stock. Moreover, the profits from prize money and 'good voyages' enabled a number of naval officers to set themselves up as landed gentlemen. Sir John Narbrough, whose father had been a small tenant in Norfolk, did so well out of his naval service that he could acquire the Knowlton estate in Kent; his son was made a baronet by James II at the age of four, in recognition of the father's services, and the estate remained the property of Narbrough's descendants until 1904. In these senses, then, the navy of the Stuart kings provided one of the relatively few pathways to significant social mobility during the latter part of the seventeenth century. So although 'gentlemen captains' increasingly dominated the commissioned officer corps, it was still perfectly possible for a former cabin boy from Norfolk to hold command over a lineal descendant of the Earls of Huntingdon, the Dukes of Buckingham, and the royal house of York.* p. 133

Sidenote:

* This was in 1683/4, when Cloudesley Shovell commanded the 'Sallee squadron' and one of her subordinate captaines was Anthony Hastings, whose four times great-grand-mother, Margaret Pole, Countess of Salisbury, was executed by Henry VIII because of her proximity to the throne; an uncle of Hastings's grandfather was, for a time, one of the principal candidates to succeed Queen Elizabeth I.

Nepotism was the main means of entry to positions of command:

In the fullness of time, Charles II even sent one of his own sons into the navy. Henry Fitzroy, Duke of Grafton, born in 1663, was his son by Barbara Palmer, Countess of Castlemaine, and later Duchess of Cleveland. The king initially refused to admit paternity, but finally did so when young Henry's bushy black eyebrows, large nose and dark, languid eyes put his paternity beyond doubt.

In September 1678. at his father's request, Grafton was entered on the ship's books of the fourth rate frigate Happy Return, ... [he] served as Master of Trinity House in 1682/83, and on 13 January 1683 was apppointed Vice-Admiral of England, nominally deputy to the Lord High Admiral, in succession to the recently deceased Prince Rupert. p. 134

Officers generally gained appointments and prmotion through a system based on the workings of patronage. Courtiers, aristocrats, politicians, royal mistresses, senior naval officers, and many others, all competed to ensure that their recommendations came to the notice of those responsible for naval appointments. p. 135

Source

J. D. Davies, Kings of the sea: Charles II, James II and the Royal Navy, Seaforth 2017