This paper describes the improvements of the 3D model proposed by Trieu et al. (2010). The model was applied to simulate the pollutant transport from fish cages (group of cages located closely together that was assigned as the single point source of pollution discharge) in the river system. In contrast, the pollution discharge from both the pond culture and the cage culture was considered in the present study. Moreover, the complete suspension was modeled by calculating the concentration of particle wastes load from riverbed. Furthermore, the conservation of simulation was ensured by using the finite volume method instead of the finite difference method to solve the 2D flow field. The improved model simulated nutrient discharge from the intensive Pangasius farming in the Mekong Delta, Vietnam. The simulated output was verified with the observed data. A good agreement between the observed and simulated data proves that the improved model could help decision makers for better planning and monitoring purposes.