In this study, residence time (RT) and flushing characteristics of the Amba estuary were estimated using a 2D depth-averaged model driven by hydrodynamics resulting from the bathymetry changes due to dredging carried out for ease of navigation. The model was calibrated and verified using observed data for the estuary and the model results of tides, currents, and Lagrangian paths are in good agreement with the field observations. The spatial variability of RT evaluated by releasing 93 particles in the model domain during low water and high water slacks of spring and neap for the pre- and post-dredging scenarios in dry and wet seasons indicates very high RTs in the mouth segment during flood due to the transport of particles in the eastern shallow regions. The lower neap RTs, as compared to spring during wet season, are due to the resultant seaward transport of particles facilitated by the freshwater discharge against weak neap currents. With meager dry season river discharge the trend is reversed with high neap RTs as compared to spring. Average RTs in the Amba estuary has decreased marginally by 0.2 days after dredging. The spatial variations show that the RTs are decreased in a larger area in the post-dredging period except at central parts of open boundary and at mouths of Patalanganga estuary and Karanja creeks. Flushing time calculations for monsoon season show slight increase from 1.2 to 1.3 tidal cycles after dredging.