Groundwater flow modeling in a small-scale area requires practical techniques to obtain high accuracy results. The effectiveness of the model calibration is the most challenging for simulating the hydraulic head. In pursuit of this, we proposed an optimized groundwater flow calibration method based on the pilot point emplacement technique for a 3D small-scale area in this work. Subsequently, two emplacement structures were tested during the experimentation, the regular pilot point placement, and the middle head measurement down gradient (MHMDG) placement with two different densities. The parameter estimation (PEST) numerical code applying the kriging interpolation was used to estimate the hydraulic conductivity field by MODFLOW. Moreover, geological SGrid models were chosen for the conceptual model. Thirty-seven observation wells were used for experimental simulations to test the proposed method in a heterogeneous confined aquifer. The result shows that the small-scale modeling was complicated, and the studying area presented a significant heterogeneity in horizontal hydraulic conductivity. The middle head measurement down gradient (MHMDG) pilot point case with the larger density gave the best R-squared 0.901 and minimum residual error of 0.0053 m compared to 0.880 and 0.078 m, respectively, for the regular placement. The calibration accuracy depended on the frequency and the emplacement of the pilot point. Therefore, the initial value should be technically selected to minimize the computation burden. The proposed techniques help to improve the groundwater flow model calibration based on the pilot point methodology for groundwater resources management.
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