Where rivers near the coastline, the receiving basin begins to influence flow, and gradually varied, nonuniform flow conditions arise. The section of the river affected by nonuniform flow is typically referred to as the backwater segment, and for large lowland rivers, this portion of the river can extend many hundreds of kilometers above the outlet. River morphology and kinematics vary in the backwater segment; however, these channel properties have not been explicitly related to properties of the flow and sediment-transport fields. This study examines the influence of spatially and temporally varying flow velocity and sediment transport on channel properties for the lower 800 km of the Mississippi River, a section of the river that includes the backwater segment. Survey transects (n = 2650) were used to constrain the cross-sectional area of water flow every ∼312 m along the Mississippi River channel for eight successive intervals of water discharge. Assuming conservation of water discharge, the local flow velocity was calculated at each transect by dividing water discharge by the local measurement of cross-sectional flow area. Calculated flow velocity was converted to total bed stress using a dimensionless friction coefficient that was determined by optimizing the match between a predicted and a measured water-surface profile. Estimates for the skin-friction component of the total bed stress were produced from the values for total shear stress using a form-drag correction. These skin-friction bed-stress values were then used to model bed-material transport. Results demonstrate that in the lower Mississippi River, cross-sectional flow area increases downstream during low- and moderate-water discharge. This generates a decrease in calculated water-flow velocity and bed-material transport. During high-water discharge, the trend is reversed: Cross-sectional flow area decreases downstream, producing an increase in calculated water-flow velocity and bed-material transport. An important contribution of this work is the identification of a downstream reversal in the trend for channel cross-sectional area due to variable water discharge. By accounting for the spatial divergences in sediment transport predicted over an average annual hydrograph, we demonstrate the tendency for channel-bed aggradation in much of the backwater reach of the Mississippi River (150–600 km above the outlet); however, a region of channel-bed erosion is calculated for the final 150 km. These results help to explain the spatial variability of channel morphology and kinematics for the lower Mississippi River, and they can be extended to other lowland river systems near the coastline.