This paper reports a refined numerical study of flow and contaminant transport in the Amazonian water system near the Anamã City, Brazil, solved by a CFD software, namely Q3drm1.0 (Q3drm: Quasi-3D refinedly modeling), developed by the Authors, which can provides three depth-integrated two-equation closure turbulence model closures. The purpose of this computation is to refinedly debug and test the developed software, including the mathematical model, turbulence closure models, algorithms, and general-purpose computational codes as well as graphical user interfaces (GUI). The three turbulence models, provided by the software to close non-simplified quasi three-dimensional hydrodynamic fundamental governing equations, include the traditional depth-integrated two-equation turbulence  model, the depth-integrated two-equation turbulence  model, developed previously by the first Author of the paper, and the depth-integrated two-equation turbulence  model, developed recently by the Authors. The reported numerical computation is to solve the corresponding discretized equations with collocated variable arrangement on the non-orthogonal body-fitted coarse and fine two-levels’ grids. With the help of Q3drm1.0 software, the steady environmental flows and transport behaviours have been numerically investigated carefully; and the processes of contaminant inpouring as well as plume development, caused by the side-discharge from a tributary of the south bank (the right bank of the river), were also simulated and discussed in detail. Although the three turbulent closure models, used in this calculation, are all applicable to the natural rivers with strong mixing, the comparison of the computational results by using the different turbulence closure models shows that the turbulence  model provides the possibility for improving the accuracy of the numerical computations of practical problems.