Many of the prisoners of the Waverley were probably held in Kilmainham gaol to await transportation. They would have been escorted from the gaol to the ship by a detachment of soldiers from the garrison at Dublin.
Passengers included Lieutenant Stirling 2nd regiment, Lieutenant Jones 16th regiment and 29 rank and file of H.M. 51st regiment, 6 women and 10 children.
The Waverly departed Kingstown, Dublin on 22 February 1839 with 176 male convicts.  On the 3rd May she spoke the Lady Bute bound for South Australia, in lat 38° 45' S., long, 25° 50' E.
Surgeon James Barr
James Barr was employed as Surgeon Superintendent. He kept a Medical Journal from 14 January to 23 June 1839.
There were three cases of scurvy among the guard of the 51st regiment, two were raw recruits and the third a child. The guard were examined every other day and those with purple spots were given double allowance of lemon juice, their salt rations were stopped and preserved soup and wine substituted and they were given anti scorbutic medicine. 
Cleanliness and Routine
James Barr insisted that the prisoners keep themselves clean and they were mustered and inspected on Thursdays and Sundays. He ensured the prisons were kept clean and dry by swinging stoves. If the weather was fine, the men were obliged to be on deck unless they were in school or were unwell. He thought a great improvement could be made in the construction of prison ships by replacing the upright elm stanchions in the three hatchways, with iron bars which would provide better ventilation. 
The Waverley arrived in Port Jackson on 17 June 1839.
There were no deaths on this voyage and the prisoners generally enjoyed good health, although there were three prisoners who the surgeon considered should not have been embarked because they were already ill. Nevertheless, they were treated kindly and indulged by the surgeon when he could.
Deaths after Arrival
The first case, Cornelius Fitzgerald had suffered pneumonia when in Kilmainham jail and was sent directly to the hospital on board. In an effort to improve his health he was given food from the Captain's table and was carefully nursed the entire voyage. He had a great desire for potatoes and was given 3 or 4 daily by the doctor. He was discharged to the hospital in Sydney on arrival and died there in 1839.
The second case was Pat Crosbie who was suffering phthisis. He died in Sydney hospital in 1839. The third case, Martin Kelly, had also been unwell in gaol but speaking no English his complaints had been overlooked and he was also suffering phthisis when sent on board. According to James Barr, he had appeared broken-hearted and became gradually weaker but he had not complained and would not have done so but for one of his messmates bringing him to the hospital. He was 'a native of Tipperary, a Whiteboy, and had been engaged in several murders'. He died in Sydney hospital in 1840. 
Hyde Park Barracks
On Saturday 22nd June, His Excellency the Governor (Sir George Gipps) visited the Prisoners' Barracks at Hyde Park for the purpose of inspecting the convicts. The names of the men were called over, and they were ranged round His Excellency in a circle, when he explained to them the situation in which they were placed in regard to the term of probation they were required to serve before being assigned to private service, and the rewards held out to them, by indulgences for good behaviour.
Notes and Links
1). One of the prisoners who arrived on the Waverley was John Joseph Carrick, supposedly a Roman Catholic Monk who was transported for life for torturing a child to death in Ireland.
4). On the night 6th January 1839 when the Waverley was probably moored in Kingstown harbour there occurred a powerful windstorm that swept across Ireland and became known as The Night of the Big Wind (Irish: Oiche na Gaoithe Moire) . There was severe damage to property; including many ships in the harbour and 350 - 400 deaths occurred. (1)