Stuart set out on his second expedition 2 April 1859. With financial assistance from the Chambers Brothers and William Finke he was able to hire more men to accompany him and obtain more instruments to establish his bearings. One of the men was David Hergott, a naturalist who had served on the Babbage expedition. They set out from Oratunga and moved to Glen's Station at Leigh Creek before travelling through country previously discovered by Samuel Parry. Hergott discovered a group of springs that became Hergott Springs, later Marree.

They then headed west following Warburton's track to Finniss Springs and arrived at Chambers Creek. On the next stage of his expedition Stuart discovered a succession of good springs: Elizabeth Springs, Beresford Springs, Hawker Springs. He travelled as far north as 27° latitude, discovering the Neales River flowing into Lake Eyre North. He considered the country as good as that adjacent to Chambers Creek. Shortly after he decided to return, as he was down to the last set of shoes for his horses. The well-being of the horses was always of paramount importance to him. Following a slightly different route, another spring was found, Loudon Springs. He reached Glen's Station on 3 July.

William Kekwick joined Stuart for the third expedition, and would remain with him for all of the remaining journeys. Stuart, Kekwick and three other men left Mount Stuart, the most northerly of the Chambers' stations, on 4 October 1859. They were provisioned for three months and had 12 horses. They again travelled to Chambers Creek, discovering Priscilla Springs en route. More springs were discovered and their bearings laid down: Beresford Springs, Strangways Springs, William Springs and Fanny Springs. These would provide a secure well-watered route to the interior. Stuart explored the edges of Lake Eyre and discovered dessicated fish trapped in the salt. The expedition had reached further north into South Australia than anyone previously had. Stuart remained at Chambers Creek while Kekwick returned to Chambers' Station at Moolooloo with the reports of the land surveyed and to seek more men for a fourth expedition.

August Petermann was a talented and prolific cartographer who did much to promote discovery in Australia with his excellent maps.

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