Unlike the First Fleet, where great efforts were taken to ensure the health of the convicts, the Second Fleet was contracted to the slave-trading firm Camden, Calvert & King who undertook to transport, clothe and feed the convicts for a flat fee of £17 7s 6d per head, whether they landed alive or not. Unlike the slave trade where deaths in transit reduced profits, the contractors had little incentive to worry about conditions. Upon arrival the sickly convicts were a drain on the already struggling colony. The only agents of the Crown in the crew were the naval agent, Lieutenant John Shapcote, who died on the voyage and Captain William Hill, commander of the NSW Corps, all other crew were supplied by the firm. Hill afterwards wrote a strong criticism of the ships’ masters stating that
...the more they can withhold from the unhappy wretches the more provisions they have to dispose of at a foreign market, and the earlier in the voyage they die, the longer they can draw the deceased’s allowance to themselves.
The fleet was comprised of six ships, one Royal Navy escort, four convict ships and a supply ship. The Lady Juliana sailed on 29 July 1789 arriving at Port Jackson after a voyage lasting 309 days on 3 June 1790 before the other convict ships and is not always counted as a member of the Second Fleet. The store ship Justinian did not sail with the convict ships on 19 January 1790 (it left the following day) and arrived before them on 20 June 1790. HMS Guardian set out before the convict ships on 12 September 1789 but struck ice after leaving the Cape of Good Hope. The Surprize, Neptune and Scarborough had previously been involved in transporting slaves to North America and left England on 19 January 1790, with 1,006 convicts (928 male and 78 female) on board. They made only one stop on the way, at the Cape of Good Hope. Here 20 male convicts, survivors from Guardian, were taken on board. The three vessels made a faster trip than the First Fleet, arriving at Port Jackson in the last week of June 1790, three weeks after Lady Juliana and a week after the Justinian.
The voyage was relatively fast, but the mortality rate was the highest in the history of transportation to Australia. Of the 1,026 convicts who embarked, over a quarter, 267 (256 men and 11 women), died during the voyage. On Neptune they were deliberately starved, kept heavily ironed and frequently refused access to the deck. Scurvy could not be checked. On Scarborough, rations were not deliberately withheld, but a reported mutiny attempt led to the convicts being closely confined below decks. On arrival at Port Jackson, half naked convicts were lying without bedding, too ill to move. Those unable to walk were slung over the side. At least 488 sick were landed (47% of those embarked). The remainder were described as ‘lean and emaciated’ and exhibiting ‘more horrid spectacles than had ever been witnessed in this country’.  Among the arrivals on the Second Fleet were D’Arcy Wentworth and his convict mistress Catherine Crowley, on Neptune and John Macarthur, then a young lieutenant in the NSW Corps and his wife Elizabeth, on Scarborough.
Map of Sydney Cover, 1788
When news of the horrors of the Second Fleet reached England, both public and official opinion was shocked. An enquiry was held but no attempt was made to arrest Donald Traill, master of Neptune and described as a demented sadist or bring a public prosecution against him, the other masters, or the firm of contractors. They had already been contracted by the government to prepare the Third Fleet for sailing to Port Jackson in 1791. Traill, along with his Chief Mate William Ellerington, were privately prosecuted for the murder of an un-named convict and also a seaman named Andrew Anderson and a cook named John Joseph. But, after a trial lasting three hours before Sir James Marriott in the Admiralty Court, the jury acquitted both men on all charges ‘without troubling the Judge to sum up the evidence.’
The Third Fleet consisted of 11 ships that set sail from United Kingdom in February, March and April 1791 bound for the Sydney penal settlement, with over 2,000 convicts.  The first ship to arrive in Sydney was the Mary Ann with its cargo of female convicts and provisions on the 9 July 1791. The Mary Ann could only state that more ships were expected to be sent. The Mary Ann had sailed on her own to Sydney Cove, and there is some argument about whether she was the last ship of the Second Fleet, or the first ship of the Third Fleet. The ships that make up each Fleet, however, are decided from the viewpoint of the settlers in Sydney Cove. For them the second set of ships arrived in 1790 (June), and the third set of ships arrived in 1791 (July-October). The Mary Ann was a 1791 arrival. The next ship to arrive just over 3 weeks later on 1 August 1791 was the Matilda. With the Matilda came news that there were another nine ships making their way for Sydney, and which were expected to arrive shortly. The final vessel, the Admiral Barrington, did not arrive until the 16 October nearly eleven weeks after the Matilda, and fourteen weeks after the Mary Ann. 194 male convicts and 4 female convicts died during this voyage. Though this death rate was high, it was nowhere near as bad as that which had occurred on the Second Fleet.
Phillip now had more mouths to feed and to avert another famine, hired the transport Atlantic to sail to Calcutta for a cargo of rice. She sailed late in October and with good sailing was expected to return by the following April or May. By early 1792, food stocks were down to dangerous levels. The grain harvest at Parramatta had been above expectations, but still too small to feed the colony for more than a few weeks. Phillip had no choice but to reduce the ration yet again. Food shortages lead to desperation and food stealing became common. Discontent became so close to revolt that the Governor refused close assembly in numbers for any reason. A numbers count revealed that 44 men and women were missing. Most had wandered into the bush, believing that they could find a better place; few were ever found or returned. In April 1792, with no sign of the Atlantic, Phillip reduced the ration again to near starvation level with flour down to 1½ pounds and 2 pounds of maize and some pork. The mortality rate had reached desperate proportions and a general air of despair was everywhere. ‘Distressing as it was to see the poor wretches dropping into the grave’, David Collins wrote,
...it was far more afflicting to observe the countenance and emaciated persons of many who remained, soon to follow their miserable companions...It was not hard labour that destroyed them; it was an entire want of strength in the constitution to receive nourishment, to throw off the debility that pervaded their whole system.
The Atlantic finally returned from Calcutta with a cargo of rice and other food including pork; the latter found to be ‘for the most part putrid’ and had to be thrown out. Phillip though, had good reason to believe that the worse was over. HMS Gorgon had returned from England with assurances from authorities that regular shipments of food and other supplies would be forthcoming. The first sign of this promise was the arrival in July, of the supply ship Britannia with four months of flour and eight months of beef and pork ‘for every description of persons in the settlement at full allowance.’ It also carried a year’s supply of clothing and the news that two more ships were on the way. The full standard ration was thereby restored.
When Phillip left the colony in December 1792, its population was 4,222, of which 1,256 were at Sydney, 1,845 at Parramatta and 1,121 at Norfolk Island. The colony was still short of many necessities and livestock. However, more than 1,700 acres of land were under cultivation or cleared of timber for cultivation. Many settlers were able to keep themselves, and some had surpluses of grain and vegetables to sell. The harvest before Phillip’s departure had yielded 4,800 bushels and within another year, Grose optimistically but prematurely reported that the colony was virtually independent of outside supply.
 William Grenville to Phillip, 24 December 1789, HRNSW, Vol. 1, (2), pp. 284-286 informed Phillip of the new batch of convicts.
 While the contract for the First Fleet had been a generous £54,000 for seven ships carrying a thousand convicts and marines, Camden, Calvert & King were paid £22,370 for four ships. Hill argued that the appalling conditions were a consequence of the contract with slaver-traders.
 Flynn, Michael, The Second Fleet: Britain’s Grim Convict Armada of 1790, (Library of Australian History), 1993, ibid, Bateson, Charles, The Convict Ships 1787-1868, pp. 120-131.
 Captain Hill to Wathen, 26 July 1790, HRNSW, Vol. 1, (2), p. 367. The recipient of the letter was the abolitionist William Wilberforce. The anguished nature of the complete letter suggests that he tried but failed to alleviate the suffering of the convicts though it was perhaps Hill’s intervention that resulted in his ship, the Surprize losing only 14 per cent of its cargo while the Neptune and Scarborough lost twice as many. See also, the extract from a letter, Rev R. Johnson to Mr Thornton, HRNSW, Vol. 1, (2), pp. 386-389.
 On the Lady Juliana see, Rees, Siân, The Floating Brothel: the extraordinary true story of an eighteenth-century ship and its cargo of female convicts, (Hodder), 2001.
 Commanded by Lieutenant Edward Riou, it struck an iceberg off the African coast. Riou, after parting with as many of his men as the boats would hold, not only successfully navigated his half-sinking ship 400 miles to the Cape of Good Hope but kept order amongst the panic-stricken convicts, an achievement that has few parallels in naval history. See, Riou to Stephens, 20 May 1790, HRNSW, Vol. 1, (2), pp. 336-340.
 Phillip’s initial response can be found in Phillip to Grenville, 13 July 1790, HRNSW, Vol. 1, (2), pp. 354-356.
 Admiralty Proceedings on the Sessions held 7th and 8th June 1792 before Sir James Marriott and others, Trials of Kimber, Traill, Ellerington and Hindmarch for murder and Berry and Slack for piracy, London, 1792
 Ibid, Bateson, Charles, The Convict Ships 1787-1868, pp. 131-139 and Ryan, R.J., The Third Fleet Convicts: an alphabetical listing of names, giving place and date of conviction, length of sentence, and ship of transportation, (Horwitz Grahame), 1983
 New Holland Morning Post, 18 October 1791.
 The problem was evident in a letter from Phillip to Lord Grenville, 5 November 1791, HRNSW, Vol. 1, (2), pp. 532-541.
 See, Phillip to Henry Dundas, 19 March 1792, Phillip to Nepean, 29 March 1792, HRNSW, Vol. 1, (2), pp. 596-599, 610-613.
 Ibid, Collins, David, An account of the English colony in New South Wales, p. 207.