In general, a groundwater aquifer is hydrogeologically non-uniform due to its inherent formation. Although numerical simulation of mass transport plays an important role for prediction and remediation of pollution, studies on macroscopic dispersion from a hydrogeological point of view are insufficient. In the present paper, a method for estimating the parameters used in a geostatistical model of logarithmic hydraulic conductivity is proposed and applied for a tracer test carried out in the aquifer of Horkheimer Insel, Germany. The macroscopic dispersion coefficient obtained by the present method agrees well with the one observed in the tracer test. It is shown that the present method is useful for evaluating the non-uniform hydrogeological structures and the macroscopic dispersion.