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The shallow subsurface bulk electromagnetic properties of the soil strongly depend on the soil water content (SWC). These properties influenced the shape, amplitude, and duration of the early-time portion of the ground-penetrating radar (GPR) signal. No-tillage and deep ploughing, two different cultivation methods, give different impacts on soil and water conservation and corn yield. Under natural field conditions, different cultivation methods can exacerbate soil lateral heterogeneity and changes in water content. In this context, we assess the capacity of the amplitude of ETS to estimate the water content of heterogeneous soil. The average envelope amplitude (AEA) of ETS of GPR response are used to estimate the SWC. The SWC estimation was conducted in two adjacent farmlands with different heterogeneities, which were caused by different cultivation methods. The results of the field experiment indicate that the soil heterogeneity can have an impact on the estimation of SWC using EST, with an error lower than 3%.