The objective of this study is to estimate 2-D spatial distribution of hydraulic conductivity (Ks) of Zhuoshui River alluvial fan, Taiwan, using groundwater level data from 88 wells and stream stage data from 4 gauging stations. In order to accomplish this analysis, wavelet analysis is first carried out to investigate the periodic cycles of groundwater level, precipitation, and stream stage. The results of the analysis show that variations of groundwater level and stream stage are highly correlated in terms of seasonal and annual periods. Subsequently, seasonal variations of groundwater level in response to stream stage variation are utilized to estimate the Ks spatial distribution by spatiotemporal cross correlation analysis, cokriging, and river stage tomography. Prior to applications of these methods to the alluvial fan, performances of each approach are evaluated and compared with reference field of a noise free synthetic experiment. It is found that all of the approaches could yield similar general spatial pattern of Ks. Nevertheless, river stage tomography seems to reveal a higher resolution of spatial Ks distribution. When the geologic zones are provided in river stage tomography analysis as prior information, the accuracy of estimated Ks values improves. Finally, results of the applications to data of the alluvial fan reveal that the apex and southeast of the alluvial fan are regions with relative high Ks and the Ks values gradually decrease toward the shoreline of the fan. These two areas are considered as the possible main recharge regions of the aquifer. It is also observed that Ks at northern alluvial fan is slightly larger than that at southern. These findings seem consistent with the geologic evolution of this alluvial fan.