We estimated annual fluxes of suspended matter and different carbon (C) pools at three sites along the lower Tana River (Kenya), based on monthly sampling between January 2009 and December 2011. Concentrations of total suspended matter (TSM), particulate organic carbon (POC), dissolved organic carbon (DOC), and dissolved inorganic carbon (DIC) were monitored, as was the stable isotope composition of the carbon pools. Both TSM and POC concentrations showed strong seasonality, varying over several orders of magnitude, while DOC and DIC concentrations showed no seasonal variations. A strong shift in the origin of POC was observed, which was dominated by C3-derived C during dry conditions (low δ13CPOC between −28‰ and −25‰), but had significant C4 contributions during high-flow events (δ13CPOC up to −19.5‰). Between Garissa and the most downstream sampling point, a clear decrease in suspended matter and organic C fluxes was observed, being most pronounced during high-discharge conditions: on an annual basis, fluxes of TSM, POC, and DIC decreased by 34% to 65% for the 3 year study period. Our results suggest that floodplains along the lower Tana River could play an important role in regulating the transport of suspended matter and organic C. A comparison of current flux estimates with data collected prior to the construction of several hydropower dams reveals that the sediment loading is reduced during low discharge conditions.