A method is proposed to estimate aquifer parameters in a heterogeneous and anisotropic aquifer under steady-state groundwater flow conditions on the basis of maximum likelihood concept. Zonation method is adopted for parameterization, and estimation errors are analyzed by examining the estimation error covariance matrix in the eigenspace. This study demonstrates the ability of the proposed model to estimate parameters and helps to understand the characteristics of the inverse problem. This study also explores various features of the inverse methodology by applying it to a set of field data of the Taegu area. In the field example, transmissivities were estimated under three different zonation patterns. Recharge rates in the Taegu area were also estimated using MODINV which is an inverse model compatible with MODFLOW.The estimation results indicate that anisotropy of aquifer parameters should be considered for the crystalline rock aquifer which is the dominant aquifer system in Korea.