Abstract: Comparing with the studies on large estuarine systems, such as the Chesapeake Bay and the San Francisco Bay, the processes of stratification and transport in small and shallow estuaries are relatively less studied. The St. Lucie Estuary (SLE) is a riverine estuary located on the east coast of south Florida. It is small and shallow, with mean depth of 2.4m. To study the estuarine processes in the SLE, a hydrodynamic model was developed based on the Environmental Fluid Dynamics Code (EFDC) [Hamrick, J.M., 1992. A three-dimensional environmental fluid dynamics computer code: theoretical and computational aspects. The College of William and Mary, Virginia Institute of Marine Science, Special Report 317, 63 pp.]. The model was calibrated and verified using observational data obtained in 1999 and 2000, respectively. The model variables used for model data-comparisons are water elevation, velocity, temperature, and salinity. The model is then applied to study the hydrodynamic processes in the SLE. It is found that freshwater inflow plays a major role in the stratification and net flushing of the SLE. Stratification generally increases with freshwater inflow. But when the inflow is persistently large for a relatively long period, the estuary can suddenly change from very stratified to well mixed within a few tidal cycles and the stratification collapses. This finding suggests that large and persistent freshwater inflows do not always increase estuarine stratification. Instead, it may cause the stratification to collapse within a short period of time. In addition to gauged tributaries, ungauged lateral inflows can also be important to small and shallow estuaries like the SLE. Although small individually, the ungauged streams and surface runoffs can be a significant portion of the total inflow and affect salinity distribution significantly. Flushing time affects a wide range of hydrodynamic and water quality processes in the estuary. The model results indicate that commonly used formulas, such as the tidal prism formula and the Knudsen formula, may significantly underestimate the flushing time. [Copyright &y& Elsevier]