Predicting morphological alterations in backwater zones has substantial merit as it potentially influences the life of millions of people by the change in flood dynamics and land topography. While there is no two-dimensional river model available for predicting morphological alterations in backwater zones, there is an absolute need for such models. This study presents an integrated iterative two-dimensional fluvial morphological model to quantify spatio-temporal fluvial morphological alterations in normal flow to backwater conditions. The integrated model works through the following steps iteratively to derive geomorphic change: (1) iRIC model is used to generate a 2D normal water surface; (2) a 1D water surface is developed for the backwater; (3) the normal and backwater surfaces are integrated; (4) an analytical 2D model is established to estimate shear stresses and morphological alterations in the normal, transitional, and backwater zones. The integrated model generates a new digital elevation model based on the estimated erosion and deposition. The resultant topography then serves as the starting point for the next iteration of flow, ultimately modeling geomorphic changes through time. This model was tested on Darby Creek in Metro-Philadelphia, one of the most flood-prone urban areas in the US and the largest freshwater marsh in Pennsylvania.