Lowland river systems (with channel slopes of 10−5 to 10−4) inevitably shift away (retreat upstream) from the receiving basin under a sustained rate of base-level rise, even if the system can maintain a period of advance at the onset of rise. This autogenic pattern of transition from progradation to retrogradation through steady base-level rise and sediment supply is termed “autoretreat.” Using a morphodynamic model of autoretreat, this study explored the varying channel hydrodynamics of lowland fluvial systems and associated stratigraphic record under sustained base-level rise and constant sediment supply. Results from the numerical simulations show that a fluvial system will reach a state of dynamic equilibrium during autoretreat where both the backwater length and the morphodynamic adjustment of the downdip channel profile become steady. Moreover, when this dynamic equilibrium state is realized, simulated systems display a persistent twofold downstream deepening of flow depth across the backwater zone, a pattern that is also present in many natural systems. In general, backwater effects play a key role in the morphodynamics of a lowland fluvial-deltaic system during autoretreat, and this hydrodynamic condition is therefore critical for predicting river responses to sea-level change.