The Navy Board was responsible for ensuring that adequate supplies of naval stores were available in the West Indies. It functioned in much the same way as the Victualling Board, hiring and loading merchant ships to carry out stores, and requesting convoys from the Admiralty. The Navy Board was represented in the West Indies by a naval storekeeper at each of the bases. It was his responsibility to forward his requirements to England periodically, to ensure that the Navy Board knew exactly what supplies were needed.

In practice, this system encountered a number of problems. First, the distance involved caused the same sort of delays as occurred with the victualling ships. Since they were usually convoyed out together, delays in the preparation of one could cause delays in the departure of the other. Secondly, unlike the Vitualling Board, the Navy Board had no theoretical framework upon which to estimate the demands in the Caribbean. All that it knew was the number and type of ships serving there, and the type and size of stores that would be required by them. It had no accurate way of estimating the rate of consumption, and this was the main reason for the frequent shortages that occurred in the West Indies. A sudden storm or hurricane could throw all normal expectations into chaos and leave the stores empty. Thirdly, the Navy Board's previous experience of fitting out ships and supplying an overseas base was of limited relevance to Jamaica, because such a large squadron had never served there before. As with the other aspects of administration, it was left to the men on the spot to make good the deficiencies as best they could.