The western branch of the East African Rift is characterized by modest amounts of extension and by deeply-subsided, fault-controlled basins filled with large, deep lakes. Lakes Tanganyika and Nyasa (Malawi) are two of the largest lakes in the world, with maximum water depths of 1450 and 700 m respectively. Newly acquired seismic reflection data, along with newly reprocessed legacy data reveal thick sedimentary sections, in excess of 5 km in some localities. The 1980's vintage legacy data from Project PROBE have been reprocessed through pre-stack depth migration in Lake Tanganyika, and similar reprocessing of legacy data from Lake Nyasa (Malawi) is underway. New high-fold and large-source commercial data have recently been collected in southern Lake Tanganyika, and new academic data have been acquired in the northern and central basins of Lake Nyasa (Malawi) as part of the 2015 SEGMeNT project. In the case of Lake Tanganyika, new data indicate the presence of older sediment packages that underlie previously identified "pre-rift" basement (the "Nyanja Event"). These episodes of sedimentation and extension may substantially predate the modern lake. These deep stratal reflections are absent in many localites, possibly on account of attenuation of the acoustic signal. However in one area of southern Lake Tanganyika, the newly-observed deep strata extend axially for ~70 km, likely representing deposits from a discrete paleolake. The high-amplitude Nyanja Event is interpreted as the onset of late-Cenozoic rifting, and the changing character of the overlying depositional sequences reflects increasing relief in the rift valley, as well as the variability of fluvial inputs, and the intermittent connectivity of upstream lake catchments. Earlier Tanganyika sequences are dominated by shallow lake and fluvial-lacustrine facies, whereas later sequences are characterized by extensive gravity flow deposition in deep water, and pronounced erosion and incision in shallow water depths and on littoral platforms. The age and provenance of the sub-Nyanja Event sequences is unknown, but may correlate to Miocene, Cretaceous or Karroo-age sedimentary packages documented elsewhere in the southwestern part of the East African Rift, including in the region around Lakes Rukwa and Nyasa (Malawi).