Most of inverse problems of groundwater flow are focused on determining the distribution of transmissivities over a flow domain from head measurements in wells under given boundary conditions. However, for groundwater management, it is important to esimate boundary flux. In this study, the technique proposed by Carrera is employed to determine the distributions of boundary fluxes as well as transmissivities from head data. The effect of zonation on the transmissivity estimation is also examined in a model where a low-transmissivity belt exists. The results show that the technique used herein is useful to estimate the boundary flux. On the other hand, the transmissivity estimation is quite sensitive to the zonation.