A high-resolution seismic survey of the Rukwa Rift has imaged the upper 300 m of the Pliocene–Holocene section. The sediments are characterized by aggradational deposition in shallow lacustrine conditions that episodically dried out. Overall the reflection package expands northeastwards towards the Lupa Fault (half-graben bounding fault). Isopach maps for nine intervals (6 m to 65 m thick) show four periods of marked expansion of the section towards the Lupa Fault, interpreted to represent times of fault activity or infilling of fault-created topography during the early stage of fault quiescence. There are three periods of little or much reduced expansion interpreted to represent infilling of the accommodation space between the lake floor and the lake surface during periods of fault inactivity. Cyclicity of such high frequency has not been widely reported for faults which penetrate the crust. The periods of activity show remarkably similar displacement patterns with no lateral migration of the main depocentre, implying that seismic and aseismic slip has persistently clustered in the same parts of the fault. Identification of high-frequency fault cyclicity has implications for sequence stratigraphy in tectonically active areas, since there is a tendency to assume faults do not have cyclic effects on the scale of tens of thousands of years.