Although all troops that were to form the second division had arrived in New York City by June 12, their departure was delayed by a shortage of transports that was not remedied until June 27. On June 30 fourteen transports escorted by Enterprise (40), Lizard (26), and Porcupine (16) sailed past Sandy Hook in a gale and headed towards Havana with 1,320 troops of the second division aboard:

58th Regiment (Anstruther's) (10 companies) 590
New York Provincial Regiment (4 companies) 477
Gorham's Rangers (2 companies)(Major Joseph Gorham) 253
Total 1,320

Albemarle and Pocock had arrived at Havana on June 6 before the first division had even embarked at New York. After not finding any sign of the North American convoys at the Cape St. Nicolas rendezvous, they had sailed on to Havana on May 27 through the Old Bahama Channel along the North coast of Cuba. The use of this channel was a bold gambit by the Admiralty to reach Havana through the most direct route. It saved time and improved the chance of surprise, but was little known and dangerous because of its narrowness and the many uncharted reefs lying just beneath the surface. No large fleet was known to have even attempted its crossing. Even so, navigational charts of the channel based upon soundings made by the Spanish San Lorenzo in 1747 fell into British hands in 1752 and emboldened the Admiralty to direct Pocock to use the channel to approach Havana.

Since the local Bahamian pilots had not proven reliable, the frigate Richmond (40) was sent ahead of the fleet with other small craft to take soundings and mark the channel by stationing small craft on both of its sides with signals in daytime and bonfires at night. The measures taken proved so effective that not even one of two hundred thirteen ship armada ran aground during the one hundred mile trajectory through it. [154]

Pocock left Port Mahon (20) stationed at the Cape St. Nicolas rendezvous and Hampshire (50) cruising the Mayaguana Passage in the southeastern Bahamas waiting for the New York convoys with letters to their commanders stating " I hope several of the masters of the transports from New York are acquainted in the Old Straits ...I am sorry not to able to leave any pilots ... If you think it too hazardous to come through the Old Straits of Bahama, you must in that case proceed with the convoy down the south side of Cuba and so round to the Havana.." The failure of the North American convoys to carry any pilots familiar with the channel or to even receive these instructions would make their Old Bahama Channel crossing a totally different experience.

There were dangers other than just navigational obstacles lurking for the American convoys in the Caribbean. On January 24 a French fleet of seven ships of the line and four frigates with two thousand infantry aboard had left Brest under the command of Rear Admiral Comte de Blenac. It arrived off Martinique on March 9 only to find that island already surrendered to the British, so it sailed on to Cape Francois on the North coast St. Domingue. Blenac's passage had not gone unnoticed and his presence so close to the Cape St. Nicholas rendezvous created a new menace to the North American convoys. On May 6 Pocock sent a message to New York advising that the Americans should stay clear of Cape Francois in coming down to the rendezvous point. This message was repeated in the letters for the convoys left with Port Mahon and Hampshire. Other than providing these warnings Pocock did not make any other dispositions to provide the North American contingent with additional security against the French threat.

As early as June 17 Albemarle was pining at Havana for the arrival of the New York convoys: "I wish the North Americans were arrived, we want them much...". His tone grew more concerned when another month passed with no account of their fate: "...if the North Americans do not arrive, and very soon, I shall be at a great loss how to proceed." The plan for the capture of the city called for first taking El Morro fortress on the East side of its harbor entrance by formal siege. This orthodox but slow course of action accepted the risk that tropical disease would cause a substantial number of casualties. Albemarle's brother, Major-General William Keppel, [155] who was in charge of the siege operations against El Morro, concurred that "The sickness among the troops still increases; the arrival of the North Americans are become absolutely necessary to our future success and that very soon to be (of) use." Yellow fever, the bane of all European troops campaigning in the tropics, had begun to take its toll on Albemarle's army. His desperation grew as his force dwindled more from disease than from combat with the North Americans offering the only hope for relief.

The journey of the first division from New York to Havana started routinely but nearly turned into a catastrophe. When it reached the Mayaguana Passage, Hampshire was not found on station and none of the warnings that Pocock had taken care to provide were passed on. [156] The commanders of the convoys for both divisions had been ordered that upon failing to make contact at the rendezvous they were "...then to make the best of your way through the Old Straits of Bahama towards Havana..." When Pocock's main fleet had sailed through the channel Captain John Elphinston of the Richmond had been instrumental in laying out the course that the fleet had safely followed.

On July 14 Pocock sent Elphinston back through the straits to seek out the first division. Before contact could be made, the commander of the first division convoy, John Hale of Intrepid, had decided to take his chances with the channel. The first reverse occurred on July 21 when the transports Juno and Masquerade carrying 279 Connecticut troops ran ashore at Cayo Confites on the North coast of Cuba at the western entrance of the channel. Masquerade was refloated but Juno was lost, however the 121 men aboard her managed to get safely ashore. Hale ordered Chesterfield to rescue the stranded men but the frigate was unable to do so because of heavy seas. In order to be able to proceed without abandoning the men, Hale decided to transfer the Connecticut soldiers on the transport Falls to his flagship so that Falls could wait for the surf to subside and then pick up the shipwrecked men, allowing Hale to sail on with the rest of the convoy. After a wait of several days, Falls succeeded in its rescue and eventually made its own way to Havana.

As the convoy proceeded through the narrowest stretch of the channel tragedy struck again just before daylight on July 24 when Chesterfield and the transports Masquerade, Industry, Smiling Nancy, and Swallow all wrecked on reefs at Cayo Romano on the North coast of Cuba. It soon became apparent that all five ships would not be saved so 594 men aboard them from the 46th and Connecticut regiments and Chesterfield's marines were disembarked on two barren cays, all without casualties. The loss of five more ships made it impossible to embark the marooned men aboard the remaining eleven vessels so Hale decided to salvage everything possible from the wrecks to sustain the men until empty transports could later be sent to rescue them. That afternoon he again pressed forward to Havana with his ever-diminishing squadron.