Transport time scales are key parameters for understanding the hydrodynamic and biochemical processes within estuaries. In this study, the flushing and residence times within the Arvand River estuary have been estimated using a two-dimensional hydrodynamic model called CE-QUAL-W2. The model has been calibrated and verified by two different sets of field data and using the k-ε vertical eddy diffusivity scheme. Flushing time has been estimated using different methods such as the tidal prism and fraction of freshwater methods. Moreover, residence times have been investigated using pulse residence time, estuarine residence time and remnant function approaches. The results have shown that different methods yield different time scales, and freshwater inflow has the greatest impact upon estimation of residence time, whereas tidal circulation hardly contributes to residence time at all. It has also been shown that the neap-spring circulation and start phase of simulations have negligible effects on the Arvand's time scales. The investigation of bathymetry showed that two sills of the estuary tend to significantly increase residence time. Understanding the applicability of these time scales and their estimation approaches helps us to evaluate the water quality management of estuaries.