Anthropogenic modifications to estuarine topography can alter hydrodynamics and affect basic processes like circulation and salinity distribution. Over the past century, the Mobile Bay ship channel has been extensively deepened and widened to accommodate larger vessels, transforming it into a pronounced channel-shoal estuary. To investigate the impact of these changes on the estuary’s hydrodynamics, unstructured 3-D hydrodynamic models were developed for the system under both historical ‘mild-modified’ and contemporary ‘severe-modified’ conditions. A recent one-year period covering a wide range of forcing conditions was used to compare and contrast the hydrodynamic behavior of the two systems. Results show that the modifications have significantly altered tidal and non-tidal dynamics, circulation, and both horizontal and vertical salinity gradients. Changes in tidal constituent amplitudes and phases have modified tidal currents. Increased residual circulation and associated salt flux have elevated salinity by up to 10 psu in the upper channel, extending the salinity intrusion by nearly 10 kilometers. The salt intrusion was more responsive to discharge variations in the historical case. In the contemporary condition, the salt front position was found to be less variable, making salt removal more challenging. Additionally, increased salinity in the channel under modern conditions have intensified lateral salinity gradients via differential advection between channel and shoals, enhancing lateral baroclinic circulation. Overall, the shift in Mobile Bay's hydrodynamics due to channel deepening and widening has been significant, underscoring the profound effects of extensive channel modifications on estuarine dynamic.