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The quality of freshwater input from tributaries of the Western Mississippi Sound (WMSS) impacts the quality of coastal water. Hydrological and hydrodynamic models can be coupled to assess the impact of freshwater inflow from coastal watersheds. This study aims to compare the performance of a hydrodynamic model and a hydrological–hydrodynamic coupled model in detecting the effect of freshwater inflow from the coastal watersheds of the state of Mississippi into the WMSS. A hydrological model, the Soil and Water Assessment Tool (SWAT), and a hydrodynamic model, the visual Environmental Fluid Dynamics Code (vEFDC), were coupled to evaluate the difference between the hydrodynamical modelling approach, which employs an area-weighted approach to define flow and nutrient concentrations, and the more recent coupling model approach, which uses a hydrological model to determine the flow and nutrient load of the model. Furthermore, a nutrient load sensitivity analysis of the effect of freshwater inflow on water quality in the WMSS was conducted in addition to assessing the repercussions of tropical depressions. Hydrological assessments of the major tributaries watersheds of Saint Louis Bay (SLB) at the WMSS were performed using the SWAT model. After calibration/validation of the SWAT model, the streamflow output from the SWAT was incorporated into the vEFDC model. Finally, hydrodynamic simulation of the SWAT-vEFDC model was conducted, and water quality output was compared at different SLB locations. The salinity, dissolved oxygen, total nitrogen (TN), and total phosphorus (TP) were assessed by comparing the vEFDC and SWAT-vEFDC outputs. The results indicated that hydrological input from the SWAT alters the flow and nutrient concentration results as compared to an area-weighted approach. In addition, a major impact on the concentration of TN and TP occurred at the location where the freshwater flows into SLB. This impact diminishes further away from the point of freshwater inflow. Moreover, a 25% nutrient load variation did not demonstrate a difference in water quality at the WMSS besides TN and TP in a post-tropical depression scenario. Therefore, the SWAT-vEFDC coupled approach provided insights into evaluation of the area-weighted method, and of hydrological model output to the hydrodynamical model, the effect of freshwater inflow into coastal waters, and nutrient sensitivity analysis, which are important for integrated coastal ecosystems management. Full article