This study aimed at determining the distribution of hydraulic conductivity and radius of influence from the results of multi-well pumping test and natural distribution of piezometric head in a non-uniform phreatic aquifer. The inverse analysis was performed by using the Fast Fourier Transform (FFT) and the constrained simplex method. These results showed that the method presented here could estimate mean value of hydraulic conductivity and the radius of influence more accurately than the conventional method using an analytical model of aquifer flow. And the distribution of hydraulic conductivity were well reproduced except the case of that the heterogeneity of hydraulic conductivity was not reflected in the distribution of drawdown and piezopmetric head.