The Northern Kenya Rift is an important natural laboratory for understanding continental rifting processes. However, much of the current understanding of its geological evolution is based on surface outcrops within footwall highs due to a lack of subsurface geological constraints. In this paper, we present an investigation of the Cenozoic stratigraphy and volcano-tectonic relationship of the volcanic sequences within the Turkana Depression (namely the North Lokichar, North Kerio and Turkana Basins). We integrate regional seismic reflection data collected as part of ongoing petroleum exploration in the area with lithological and biostratigraphic data from new wells that were drilled in 2014 and 2015 (Epir-1 and Emesek-1). This has allowed linking and extrapolation of the detailed stratigraphy of the paleontologically important Lothagam site to the volcanic sequences within the Napedet Hills, North Lokichar, North Kerio and Turkana Basins. The site of the Plio-Pleistocene-age Turkana Fault, which separates the North Lokichar Basin from the Turkana and North Kerio Basins, appears previously to have acted as a focus of Middle Miocene volcanism c. 5 Ma prior to the main period of movement on the fault. Our study highlights how subsurface and outcrop information can be combined to give a more in-depth knowledge of the magmatic history within rift basins.