Hydraulic tomography is a cost-effective technique for characterizing the heterogeneity of hydraulic parameters in the subsurface. During hydraulic tomography surveys a large number of hydraulic heads (i.e., aquifer responses) are collected from a series of pumping or injection tests in an aquifer. These responses are then used to interpret the spatial distribution of hydraulic parameters of the aquifer using inverse modeling. In this study, we developed an efficient sequential successive linear estimator (SSLE) for interpreting data from transient hydraulic tomography to estimate three-dimensional hydraulic conductivity and specific storage fields of aquifers. We first explored this estimator for transient hydraulic tomography in a hypothetical one-dimensional aquifer. Results show that during a pumping test, transient heads are highly correlated with specific storage at early time but with hydraulic conductivity at late time. Therefore reliable estimates of both hydraulic conductivity and specific storage must exploit the head data at both early and late times. Our study also shows that the transient heads are highly correlated over time, implying only infrequent head measurements are needed during the estimation. Applying this sampling strategy to a well-posed problem, we show that our SSLE can produce accurate estimates of both hydraulic conductivity and specific storage fields. The benefit of hydraulic tomography for ill-posed problems is then demonstrated. Finally, to affirm the robustness of our SSLE approach, we apply the SSLE approach to a hypothetical three-dimensional heterogeneous aquifer.