A three-dimensional flow and temperature model was applied for a 124 km river-reservoir system from Lewis Smith Dam tailrace to Bankhead Lock & Dam, Alabama. The model was calibrated against measured water levels, temperatures, velocities and flow rates from 4 May to 3 September 2011 under small constant release (2.83 m 3 /s) and large intermittent releases (~140 m 3 /s) from an upstream reservoir. Distributions of simulated flow and temperatures and particle tracking at various locations were analyzed which revealed the complex interactions of density currents, dynamic surface waves and solar heating. Flows in the surface and bottom layers moved in both upstream and downstream directions. If there was small constant release only from Smith Dam, simulated bottom temperatures at Cordova were on average 4.8°C higher than temperatures under actual releases. The momentum generated from large releases pushed bottom density currents downstream, but the released water took several days to reach Cordova.

Authors collaborated together for the completion of this work. Author JD designed the study, developed and calibrated the Perdido EFDC model, ran the model for all cases, performed data analyses of model results and wrote the first draft of the manuscript. Author XF provided valuable instructions on study design, supervised the data analyses, and reviewed and revised the manuscript. Author VZF contributed by revising and improving the manuscript and interpreting model results due to the sea level rise. All authors read and approved the final manuscript.

A three-dimensional Environmental Fluid Dynamics Code model was developed for a 17-km segment of the Mobile River, Alabama, USA. The model external forcing factors include river inflows from upstream, tides from downstream, and atmospheric conditions. The model was calibrated against measured water levels, velocities, and temperatures from 26 April to 29 August 2011. The Nash-Sutcliffe coefficients for water levels were greater than 0.94 and for water temperatures ranged from 0.88 to 0.99. The calibrated model was extended approximately 13 km upstream for simulating unsteady flow, dye, and temperature distributions in the Mobile River under different upstream inflows and downstream harmonic tides. Velocity profiles and distributions of flow, dye, and temperature at various locations were analyzed and show that flow recirculation could only occur under small inflow (50 m 3 s-1) when downstream tides control the flow pattern in the Mobile River. The model results reveal complex interactions among discharges from a power plant, inflows, and tides.

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A calibrated three-dimensional hydrodynamic model was applied to study subtidal water and salt exchanges at various cross sections of the Perdido Bay and Wolf Bay system using the Eulerian decomposition method from 6 September 2008 to 13 July 2009. Salinity, velocity, and water levels at each cross section were extracted from the model output to compute flow rates and salt fluxes. Eulerian analysis concluded that salt fluxes (exchanges) at the Perdido Pass and Dolphin Pass cross sections were dominated by tidal oscillatory transport FT, whereas shear dispersive transport FE (shear dispersion due to vertical and lateral shear transport) was dominant at the Perdido Pass complex, the Wolf-Perdido canal, and the lower Perdido Bay cross sections. The flow rate QF and total salt transport rate FS showed distinct variation in response to complex interactions between discharges from upstream rivers and tidal boundaries. QF and FS ranged from −619 m