With Kenyan independence (1963) Dr Harthoorn's position as senior lecturer at the veterinary college in Nairobi was abruptly terminated (he was replaced without notice by one of his PhD students). He moved to South Africa and continued his work with large African mammals, including elephant and rhinoceros transport. His work was absolutely vital in the creation of many South African game reserves, in particular the Hluhluwe–iMfolozi Park reserve in northern Kwazulu-Natal, where his work with Ian Player was vital in preserving the white rhinoceros. He also had a vital role in the saving of thousands of animals marooned on small islands created by the rising waters of the newly formed Kariba Dam in 1959-1960 in Southern Rhodesia (Zimbabwe). The campaign to save the animals was dubbed Operation Noah.