One of type's surface water-groundwater systems is the stream-aquifer system. Simulation of solute traort in a stream-aquifer system is composed of two main components. Theses are the simulation of water movement and the simulation of solute traort. The first component incorporates groundwater flow in the aquifer, surface flow in the stream, flow interaction between the aquifer and the stream. The Second component incorporates solute traort in the aquifer, solute traort in the stream, and the solute interchange between the stream and the aquifer. In this research, qualitative simulation of a complex hydrosystem including of Koohpayeh-Segzi aquifer and Zayandehrud River passing from it has been studied. Considering the fact that major activity in this region is the agriculture, the most important source contaminant of the aquifer are agriculture effluents that cause to increase exist cations and anions concentration, especially chloride, sodium, calcium and magnesium. Considering the fact that these contaminants are utterly soluble, TDS is selected as qualitative index variable. Because of conservative nature of contaminants, predominant mechanisms in solute traort within the porous media and river are advection and dispersion mechanisms. Qualitative simulator model of this complex hydrosystem has run in the unsteady state for five stress periods. After calibration of the qualitative model in this complex hydrosystem, obtained results from this simulator model were compared with gathering samples of observation wells, and the validation of simulation was confirmed. Also consequences of sensitivity analysis for dispersivity coefficient parameter in shallow and deep aquifers demonstrated that model is not sensitive with respect to this coefficient. In other words predominant mechanism in solute traort in this complex hydrosystem is advection mechanism. Furthermore with investigation and analysis of model outputs, the fundamental and key role of Zayandehrud River in affecting on water quality of aquifer is confirmed.