Tropical inland waters are increasingly recognized for their role in the global carbon cycle, but uncertainty about the effects of such systems on the transported organic matter remains. The seasonal interactions between river, floodplain, and vegetation result in highly dynamic systems, which can exhibit markedly different biogeochemical patterns throughout a flood cycle. In this study, we determined rates and governing processes of organic matter turnover. Multi-probes in the Barotse Plains, a pristine floodplain in the Upper Zambezi River (Zambia), provided a high-resolution data set over the course of a hydrological cycle. The concentrations of oxygen, carbon dioxide, dissolved organic carbon, and suspended particulate matter in the main channel showed clear hysteresis trends with expanding and receding water on the floodplain. Lower oxygen and suspended matter concentrations prevailed at longer travel times of water in the floodplain, while carbon dioxide and dissolved organic carbon concentrations were higher when the water spent more time on the floodplain. Maxima of particulate loads occurred before highest water levels, whereas the maximum in dissolved organic carbon load occurred during the transition of flooding and flood recession. Degradation of terrestrial organic matter occurred mainly on the floodplain at increased floodplain residence times. Our data suggest that floodplains become more intense hotspots at prolonged travel time of the flood pulse over the floodplain.