The objective of this study is to analyze nonlinear wave-current interaction directly using LES-WASS-3D. The fully-nonlinear three-dimensional numerical model LES-WASS-3D is upgraded with the addition of salinity and temperature advection-diffusion equation. The numerical simulation was conducted with the consideration of wave in the estuary area with currents from river. Based on the results of the numerical simulation, the wave influence of salt water wedge and fresh water diffusion is discussed.