The aim of this paper is to study the popular models used for the simulation of major elements of a water quality system. The present study compares results of the CE-QUAL-W2 model with the WASP5 and MIKE11 models to assess the water quality of Pasikhan River. The contaminant loadings of Nitrate and Phosphate are utilized in the CE-QUAL-W2, WASP5 and MIKE11 simulations. This study is the first report of the innovative use of three commonly used numerical models for selecting a suitable tool to simulate the rivers water quality. All three simulated models measured data reasonably well. The sensitivity analysis for CE-QUAL-W2 model shows that the model is highly sensitive to the Manning coefficient and point source flow rate. The calibrated model responses are in good agreement with the field data and can be used as scenario generators in a general strategy to conserve or improve the water quality. During the period of intense stratification, predictions from CE-QUAL-W2 are inconsistent better to the measured data than those from Mike11 and WASP5 due to the improved transport scheme used in CE-QUAL-W2. In general, CE-QUAL-W2 offers significant advantages over Mike11 and WASP5 in simulations of water quality in the Pasikhan River.