The greatest difficulty faced by a commander–in–chief in the West Indies was manning his ships. This went hand in hand with the problems of sickness and desertion. Sickness was the biggest single cause of ships being short of complement. Much of the effort expended trying to cure the sick was aimed at recovering as many men as possible for the service. Manning was also indirectly affected by sickness. The unhealthy climate gave the Caribbean such a bad name that few were willing to serve there voluntarily, and those compelled to do so were often more prepared to risk punishment for desertion, than to wait for death from yellow fever.

The readiness of seamen to desert was equally serious, particularly in wartime, when the captains of merchant ships, and privateers desperate for crews, were often prepared to help deserters evade the clutches of the navy. As many of the owners of such ships were prominent men in the islands, the commander–in–chief did not always receive the assistance he expected to recover them. This led to friction between the civil and naval authorities, which in Jamaica culminated in an unseemly brawl between the governor and an admiral.

The problem of manpower wastage was compounded by the very limited recruiting options open to the navy. The only source of trained men was the merchant fleet and privateers, and no volunteers could be expected from there. The alternative recourse of the pressgang also raised problems, since its legality was seriously questioned in the West Indies, and its employment caused further friction with the civil powers.