The goal of this study was to explore the archaeology of farming communities on the northern shores of Lake Victoria Nyanza, Uganda. The study explored the process of transition to farming, and the settlement history and subsistence structures of communities of both the Late Stone Age (LSA) and the Early Iron Age (EIA). Further, the study explored the LSA–EIA relationship and compared the archaeology of the northern shores of Lake Victoria Nyanza with the archaeology, as it is widely understood, of the lake’s eastern and western shores. The study used survey, excavation, flotation, and dating methods to collect data from the Busia and Namayingo districts. It also performed ceramics, lithics, bone point, stable isotope, osteoarchaeological, faunal, and botanical analyses. The study identified 24 new archaeological sites of which five were excavated—three were Kansyore LSA sites, one was an LSA–EIA site, and one was a Late Iron Age (LIA) site. Well-preserved LSA and EIA burials dating from 6634 to 6479 BC and from AD 339 to 437 were excavated systematically for the very first time in Uganda. Further, the study identified a new Kansyore phase, namely, the Middle Kansyore phase, dating from 3465 to 3495 BC. This study was the first of its kind to confirm the presence of ceramic hunter-gatherers and EIA farmers in the study area and to indicate that there was no evidence of contact between the Kansyore LSA communities and the later EIA communities. Further, the study offered insights into the lifeways of each group and clearly indicated that the transition to farming resulted from a combination of factors such as population movements and the environment. The outcomes of this study contributed directly to the big debate on the regional and global understanding of the transition to farming. The study concluded that the northern shores of Lake Victoria Nyanza had been occupied by Pre-ceramic hunter-gatherers, Kansyore LSA and EIA to LIA farming communities who had had no contact with their predecessors. Although information on this area has the potential to provide answers to many future questions about the lifeways of past communities, this potential may be thwarted by the activities of harvesters who operate in the area and depend on the harvesting of sand and shells to make a living. This study recommends that the government should emphasise the importance of cultural impact assessments to be conducted by companies involved in mining or any other development that is likely to hinder the survival of cultural sites. This study had to make use of purposive survey approaches because of limited funds and time, as a result of which most of the sites in the area under study remained unknown archaeologically; therefore, future researchers should conduct surveys in this area. Finally, sensitisation of the locals about the importance of preserving their culture and heritage should be part and parcel of every future project to avoid site destruction by local people.