The royal navy had provided the real teeth of the maritime campaigns against the Jacobites, and the multi-faceted system of authority for mixed Scottish and English forces under English naval commanders, and broader operational control by Scottish generals or privy councillors, seemed to have worked well. However, the 1690s also saw a crisis of authority. An embargo on trade with France was enforced zealously by the navy, which seized any ships that broke it, including Scots. Such seizures, often near their home ports, were denounced by Scottish privy councillors then, and historians since, as an assault on Scottish sovereignty. There is an alternative view, that Scotland had signed up to the embargo, and the royal navy was therefore right to enforce it.

Scotland had arguably been giving up a portion of its maritime sovereignty ever since the royal navy's participation in Ochiltree's expedition, but as many Scots found the embargo on an important trading partner irksome, this consequence of reliance on outside naval support was now exposed. A commonality between conflicts within seventeenth-century composite monarchies was the imposition of ‘nov-elties’ upon a peripheral part of the monarchy, and the resistance to that by reference to the ‘ancient constitution’. Conflict over seizures follows this pattern, albeit not to the extreme of rebellion. The nature of the imposition in question, either at bottom an economic measure or a war-fighting one, is a source of dispute. Certainly, economic differences and barriers were a common problem in composite monarchies; for example, the persistence of customs barriers was something Olivares had wanted to tackle in 1630s Spain, but in the end, it was war fighting that was at the centre of his crisis and of this one.

Pottinger and the Navigation Acts

In the run up to union, one of its principal opponents, Andrew Fletcher, warned of the risks to Scotland of the English seeking to ‘establish in themselves the empire of the sea, with an entire monopoly of trade’. That empire, supported by England's naval power, was, to Fletcher, pushing Scotland into economic dependence, but he was aware that that same power was simultaneously the guarantee of the protestant monarchy. Edward Pottinger's 1690 campaign was a perfect encapsulation of those two aspects of English naval power.