This paper describes a numerical simulation in the Amazon water system,aiming to develop a quasi-three-dimensional numerical tool for refined modeling of turbulent flow and passive transport of mass in natural waters.Three depth-averaged two-equation turbulence closure models,(k)-(ε),(k)-(w),and(k)-(ω),were used to close the non-simplified quasi-three-dimensional hydrodynamic fundamental goving equations.The discretized equations were solved with the advanced multi-grid iterative method using non-orthogonal body-fitted coarse and fine grids with collocated variable arrangement.Except for steady flow computation,the processes of contaminant inpouring and plume development at the beginning of discharge,caused by a side-discharge of a tributary,have also been numerically investigated.The three depth-averaged two-equation closure models are all suitable for modeling strong mixing turbulence.The newly established turbulence models such as the(k)-(ω)model,with a higher order of magnitude of the turbulence parameter,provide a possibility for improving computational precision.