Seasonal flooding of riverine backwaters is important in maintaining diverse aquatic habitats, but anthropogenic impacts have reduced the frequency and duration of such flooding. This study, conducted in a 2.5-km-long shallow floodplain severed meander backwater adjacent to the Coldwater River in Tunica County, Mississippi, USA, compared water quality during a late summer 30-day artificial flooding period with 28-day pre-flood and 26-day post-flood periods. Flooding was simulated by pumping 0.22 to 0.35 m3 s−1 from the river into the upstream portion of the backwater. In situ parameters (temperature, pH, dissolved oxygen, conductivity and fluorescent chlorophyll) were measured every 30 min at one site within the backwater. Solids (dissolved and suspended) and nutrients (phosphorus and nitrogen) were measured at three sites in the backwater and in the river every 3 to 5 days. Decreases in the amplitude of temperature, dissolved oxygen and pH diel cycles within the backwater were observed during flooding. Changes in patterns of solids and nutrients were also associated with flooding. Complex patterns in phosphorus and nitrogen emerged as a result of utilization by autotrophs (measured as chlorophyll) and seasonal changes. Artificial flooding in a shallow floodplain water body stabilized and improved water quality for aquatic biota and is a viable method for habitat rehabilitation in these systems. Copyright © 2011 John Wiley & Sons, Ltd.