Dam construction in the 1960's to 1980's significantly modified sediment supply from the Kenyan uplands to the lower Tana River. To assess the effect on suspended sediment fluxes of the Tana River, we monitored the sediment load at high temporal resolution for one year and complemented our data with historical information. The relationship between sediment concentration and water discharge was complex: at the onset of the wet season, discharge peaks resulted in high sediment concentrations and counterclockwise hysteresis, while towards the end of the wet season, a sediment exhaustion effect led to low concentrations despite the high discharge. The total sediment flux at Garissa (ca. 250 km downstream of the lowermost dam) between June 2012 and June 2013 was 8.8 Mt yr−1. Comparison of current with historical fluxes indicated that dam construction had not greatly affected the annual sediment flux. We suggest that autogenic processes, namely river bed dynamics and bank erosion, mobilized large quantities of sediments stored in the alluvial plain downstream of the dams. Observations supporting the importance of autogenic processes included the absence of measurable activities of the fall-out radionuclides 7Be and 137Cs in the suspended sediment, the rapid lateral migration of the river course, and the seasonal changes in river cross-section. Given the large stock of sediment in the alluvial valley of the Tana River, it may take centuries before the effect of damming shows up as a quantitative reduction in the sediment flux at Garissa. Many models relate the sediment load of rivers to catchment characteristics, thereby implicitly assuming that alterations in the catchment induce changes in the sediment load. Our research confirms that the response of an alluvial river to external disturbances such as land use or climate change is often indirect or non-existent as autogenic processes overwhelm the changes in the input signal.