A three-dimensional (3-D) hydrodynamic model, Curvilinear-Grid Hydrodynamics in 3-D (CH3D), and observation data are used to investigate the effects of Tropical Storms Fay and Hanna in 2008 on the spatial structure of residual circulation and momentum balance inside the subtropical estuarine system of the Northern Coastal Basin and St. Augustine Inlet. During a typical tidal cycle, four residual eddies are formed: two strong eddies inside of the inlet and two weaker eddies outside of the inlet. During Tropical Storms Fay and Hanna the alongshore component of the northeasterly winds disrupted the ocean-side eddies first and forced the alongshore southeasterly current. Owing to not-so-strong local winds, residual flow at the mouth of the inlet never became complete inflow. However, following Tropical Storm Fay's landfall, flow inside the inlet became complete outflow owing to relaxing wind and the remote wind effect created by the alongshore component of the southeasterly wind. The residual circulation returned to its prestorm condition in 4 days owing to relatively short storm duration. Model results revealed that the cross-sectional residual flow pattern observed at the inlet mouth is highly variable with time and location of the cross section. Comparison of various terms in the horizontal momentum equations shows that the balance is primarily between the barotropic pressure gradient and nonlinear advection. Although the wind stress and bottom friction briefly become significant in the balance, they are still at least an order of magnitude smaller. Baroclinic pressure gradient is weak despite the increase in precipitation and river discharge.