With the expansion of the Panama Canal, ocean-going cargo vessels have increased in size to improve efficiency and carrying capacity. In order to accommodate the increasing drafts of these ships. Channel deepening projects can cause salinity intrusion into freshwater portions of the river system resulting in significant water quality impacts to the ecosystem.

A coarse-grid model of a portion of the St. Johns River was originally developed for the Jacksonville Harbor Deepening Project Feasibility Study. DCCM was contracted by the Jacksonville District USACE to develop, calibrate and validate a more comprehensive and representative hydrodynamic and salinity water quality model of the Jacksonville Harbor. The model incudes 121 miles of the St. Johns River, adjacent wetlands and freshwater tributaries. The newly calibrated and expanded 3-D hydrodynamic model was developed using a newly developed version of the Environmental Fluid Dynamics Code (EFDC) and was used to evaluate the impacts of the channel deepening on salinity intrusion and stratification in the St. Johns River. The new multiprocessor version of EFDC was used to improve runtimes and the SIGMA-ZED vertical layering option within the gridding package was used to improve computational efficiency and the simulation of vertical stratification. In order to assess navigation channel modification impacts to circulation processes and salinity in the St Johns River, DCCM performed two simulations covering a 5 year-long period (2017-2022). The first simulation represented the existing channel bathymetry without deepening and the second simulation included the with-project (channel deepened) condition. Simulated water levels, flows, velocity, water age as a measure of residence time, and salinity were compared for each simulation.

Numerous diagnostic simulations were conducted to evaluate contributions to increased salinity, difference between project induced salinity increases and salinity increases related to other processes such as freshwater flow variations, subtidal variations, offshore salinity variations, sea level rise, variations of wind velocities and directions.

To improve the simulation of freshwater contributions from the adjacent watershed, DCCM evaluated and recalibrated existing HSPF watershed model. DSLLC processed USGS flow and groundwater data for the HSPF model, recalibrated the HSPF model and extended the simulation period. DSLLC then linked the recalibrated hydrologic model results as input to the Jacksonville Harbor 3D EFDC hydrodynamic model to simulate a more natural stormwater response from freshwater tributaries. The model results with the new EFDC Pre-Project model showed improved calibration and much shorter runtimes.