Abstract-A semi-implicit and Eulerian-Lagrangian finite difference method for three-dimensionalshallow flow has been extended to a more complete system of equations incorporating second-momentturbulence closure model and transport equations of salinity and temperature. The simulation for flood-ing and drying of mudflats has been improved. The model is applied to Xiamen waters. Based on exten-sive survey data, water level elevation, temperature and salinity field along the eastern open boundaryand at the Jiulong River inlets and runoffs are analyzed, specified and calibrated. The computed resultsshow good agreement with the measured data, reproduce flooding, emergence of large and complexmudflat region. Abstract-A semi-implicit and Eulerian-Lagrangian finite difference method for three-dimensionalshallow flow has been extended to a more complete system of equations incorporating second-momenturbulence closure model and transport equations of salinity and temperature. The simulation for flood-ing and drying The model is applied to Xiamen waters. Based on exten-sive survey data, water level elevation, temperature and salinity field along the eastern open boundaryand at the Jiulong River inlets and runoffs are analyzed, specified and calibrated. The computed resultsshow good agreement with the measured data, reproduce flooding, emergence of large and complex motudt region.