In plantation areas, soil conditions affect the crop's quality. One of the crucial elements in the soil for plant survival is soil water content (SWC). Radar system has advantages that can be implemented for measuring SWC in plantation areas. A radar system operates by utilizing electromagnetic waves to obtain the dielectric characteristics of the soil. However, the presence of tea plants has become an obstacle to the radar wave propagation toward the soil layer. Reflected signal, which is influenced by the presence of vegetation, makes the estimation of SWC inaccurate. Consequently, the estimation of SWC needs to consider the vegetation's effect. This study uses an FMCW radar system, which operates at a frequency of 24 GHz. A layer medium propagation model is proposed in this study to prove the relationship between the reflected signal and the SWC. The reflection coefficient extracted from the radar signal is used to estimate the SWC. The vegetation propagation constant was obtained from the average field measurement results. The gravimetric method is used to validate the SWC estimation in vegetation's presence using the radar system. The results of the field experiments showed that the proposed method succeeded in estimating the SWC by considering the presence of vegetation with an average error of 3.57%. The proposed method has the potential to be applied to plantation areas.