Lexical borrowing may provide valuable clues about the sociohistorical context of language contact. Here we explore patterns of vocabulary transfer between languages from three families (Kx’a, Tuu, Khoe-Kwadi) comprising the linguistic unit commonly referred to as Southern African Khoisan. In our dataset, 20% of 1,706 roots are shared between at least two families. By applying a carefully chosen set of linguistic and extralinguistic criteria, we were able to trace the origin of 71% of shared roots, with the remaining 29% constituting good candidates for ancient contact or shared common ancestry of the forager families Kx’a and Tuu. More than half of the shared roots for which an origin could be determined trace back to Khoe-Kwadi and were borrowed into languages of other families within two major confluence zones with different sociohistorical profiles: i) the Central Kalahari characterized by egalitarian interaction between languages of all three families, and ii) the southern and southwestern Kalahari Basin fringes showing unilateral transfer from Khoe-Kwadi-speaking herders into resident forager groups. The findings of this study complement genetic and archaeological research on southern Africa and testify to the value of linguistics in the multidisciplinary inference of contact and migration scenarios.