Hydraulic tomography (HT) based on the successive linear estimator (SLE) offers the high-resolution characterization of aquifer heterogeneity but conventionally requires prolonged pumping to achieve steady-state conditions, limiting its applicability in contamination-sensitive or low-permeability settings. This study bridged theoretical and practical gaps (1) by identifying spatial periodicity (hole effect) as the mechanism underlying divergences in steady-state cross-correlation patterns between random finite element method (RFEM) and first-order analysis, modeled via an oscillatory covariance function, and (2) by validating a novel short-term sampling strategy for SLE-based HT using field experiments at the University of Göttingen test site. Utilizing early-time drawdown data, we reconstructed spatially congruent distributions of hydraulic conductivity, specific storage, and hydraulic diffusivity after rigorous wavelet denoising. The results demonstrate that the short-term sampling strategy achieves accuracy comparable to that of long-term sampling strategy in characterizing aquifer heterogeneity. Critically, by decoupling SLE from steady-state requirements, this approach minimizes groundwater disturbance and time costs, expanding HT’s feasibility to challenging environments.