This thesis presents a method, Ensemble Kalman Filter (EnKF), applied to a highresolution, shallow water equations model (DG ADCIRC-2DDI) of the Lower St. Johns River with observation data at four gauging stations. EnKF, a sequential data assimilation method for non-linear problems, is developed for tidal flow simulation for estimation of state variables, i.e., water levels and depth-integrated currents for overland unstructured finite element meshes. The shallow water equations model is combined with observation data, which provides the basis of the EnKF applications. In this thesis, EnKF is incorporated into DG ADCIRC-2DDI code to estimate the state variables. Upon its development, DG ADCIRC-2DDI with EnKF is first validated by implementing to a low-resolution, shallow water equations model of a quarter annular harbor with synthetic observation data at six gauging stations. Second, DG ADCIRC-2DDI with EnKF is implemented to a high-resolution, shallow water equations model of the Lower St. Johns River with real observation data at four gauging stations. Third, four different experiments are performed by applying DG ADCIRC-2DDI with EnKF to the Lower St. Johns River.