Suspended sediment is the primary source for a sustainable agro-ecosystem in the Mekong Delta by providing nutrient input for the subsequent cropping season. In addition, the suspended sediment concentration (SSC) plays an important role in the erosion and deposition processes in the Delta; that is, it influences the morphologic development and may counteract the deltaic subsidence and sea level rise. Despite this importance, little is known about the dynamics of suspended sediment in the floodplains of the Mekong Delta. In particular, quantitative analyses are lacking mainly because of data scarcity with respect to the inundation processes in the floodplains. In 2008, therefore, a comprehensive in situ system to monitor the dynamics of suspended sediment in a study area located in the Plain of Reeds was established, aiming at the characterization and quantification of suspended sediment dynamics in the deeply inundated parts of the Vietnamese part of the Mekong Delta. The monitoring system was equipped with seven water quality–monitoring stations. They have a robust design and autonomous power supply suitable for operation on inundated floodplains, enabling the collection of reliable data over a long period of time with a high temporal resolution. The data analysis shows that the general seasonal dynamics of suspended sediment transport in the Delta is controlled by two main mechanisms: the flood wave of the Mekong River and the tidal backwater influences from the coast. In the channel network, SSC decreases exponentially with distance from the Mekong River. The anthropogenic influence on SSC could also be identified for two periods: at the start of the floodplain inundation and at the end of the flood period, when subsequent paddy rice crops are prepared. Based on the results, we recommend an operation scheme for the sluice gates, which intends to distribute the sediment and thus the nutrients equally over the floodplain. Copyright © 2013 John Wiley & Sons, Ltd.