Lake Edward is single half-graben rift basin unique in the East African Rift System as a result of its connection to Lake George via the Kazinga Channel, a paleo–river valley which is incised into the flexural margin of the lake. Using recently acquired normal-incidence seismic reflection data and thirty-three lake-bottom sediment samples, we examine the consequences of this hydrologic connection for understanding depositional processes and facies development along the flexural margin of Lake Edward. Three depositional sequences were defined in the study area based on top and bottom discordances of seismic reflections. Climatically induced changes in lake level appear to have forced sequence development. Sequence I deposits indicate that highstand conditions prevailed earlier in the Pleistocene. Evidence for high-frequency lake-level change comes from lowstand delta clinoforms in two separate stratigraphic intervals on the flexural margin. An older lowstand event occurred during Sequence II time and reduced lake level by at least ~ 37 m. A younger lowstand event occurred during the deposition of Sequence III and reduced lake level by ~ 18 m. Clastic sedimentation on the flexural margin of Lake Edward is strongly modified by inflow from the Kazinga Channel and Lake George during periods of lowered lake level. We suggest that the presence of an incised valley at the margin of the rift controls the stratigraphic development of clinoforms diagnostic of lowstand deltaic sedimentation. The morphology and orientation of these clinoforms suggest that discharge from Lake George during arid periods utilized the Kazinga Channel to transport sediment toward the exposed flexural margin of Lake Edward. Dipping reflections in sigmoid-oblique clinoforms suggest that these flows were capable of transporting sediment loads that included coarse grain sizes. Deposition by this process occurred several times during the late-Quaternary history of Lake Edward, and represents an important modern analogue for linked incised valley-lacustrine delta sequences in the stratigraphic record.