On 15 February 1863 Sir Samuel and Lady Florence Baker were at Gondokoro awaiting information about the English Explorers John Speke and James Grant, who were travelling north from Zanzibar. Baker writes “At a distance I recognised my old friend Speke, and with a heart beating with joy I took off my cap and gave a welcome hurrah! For the moment he did not recognize me, my sudden appearance in the centre of Africa appeared to him incredible. He had walked the whole way from Zanzibar, never having once ridden during that wearying march. Grant was in honourable rags. Both men had a fire in the eye that showed the spirit that had led them through.” Speke and Grant had located and named Lake Victoria - that great source of the Nile.
“Upon my congratulating them with all my heart, upon the honour they had so nobly earned, Speke and Grant with characteristic candour and generosity gave me a map of their route.” They told him that they had tracked the river from Lake Victoria, but it had turned suddenly west from the Karuma Falls at which point Speke and Grant had to continue their journey north to Gondokoro. There was still a mystery to solve.
Samuel Baker and Florence set off from Gondokoro in March 1863 with a small party of 17 to find out the exact route of the Nile from the Karuma Falls until it flowed north again. It took them a year of arduous travel beset by illness and many dangers to finally reach that second source of the Nile, a lake they named Lake Albert.

Later, in April 1871 Sir Samuel and Lady Florence Baker returned to Gondokoro to put down the evils of the slave trade. Baker writes “The country is sadly changed; formerly pretty villages in great numbers dotted over the landscape, beneath shady clumps of trees and the land was thickly populated. Now all is desolate; not a village exists; they have all been destroyed.” This was the work of the slavers and Sir Samuel set about denying them the chance to use Gondokoro as a route to transport their miserable trade along the Nile to Khartoum. By December Sir Samuel could report “Everything was in order in Gondokoro. There was peace; food was abundant and the station securely fortified.” So, in January 1872 Sir Samuel and Lady Florence Baker, with only a small force, set off southwards to put down the slave trade in what is now South Sudan and Uganda.