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This study shows how a cost-effective hydraulic tomography survey (HTS) and the associated data estimator can be used to characterize flow and transport in heterogeneous aquifers. The HTS is an improved field hydraulic test that accounts for responses of hydraulic stresses caused by pumping or injection events at different locations of an aquifer. A sequential data assimilation method based on a cokriging algorithm is then used to map the aquifer hydraulic conductivity (K). This study uses a synthetic two-dimensional aquifer to assess the accuracy of predicted concentration breakthrough curves (BTCs) on the basis of the Kfields estimated by geometric mean, kriging, and HTS. Such Kfields represent different degrees of flow resolutions as compared with the synthetically generated one. Without intensive experimentsto calibrate accurate dispersivities at sites, the flow field based on the HTS Kfield can yield accurate predictions of BTC peaks and phases. On the basis of calculating mean absolute and square errors for estimated K fields, numerical assessments on the HTS operation strategy show that more pumping events will generally lead to more accurate estimations of Kfields, and the pump locations need to be installed in high Kzones to maximize the delivery of head information from pumps to measurement points. Additionally, the appropriate distances of installed wells are suggested to be less than one-third of the ln(K) correlation length in x direction.