In this study, the phenological behavior and energy balance of plants are used as a sensory mechanism for root-zone soil moisture monitoring using both in-situ and satellite remote sensing data. The commonly used in-situ measurements are not feasible for mapping soil moisture at large-scale agricultural areas. Local direct root-zone soil moisture measurements cannot be reliably interpolated owing to the high spatial variability of soil structure and the vegetative content. Remote sensing methods are negatively affected by vegetation coverage and density regarding penetration and backscattering characteristics. In order to overcome these limitations, we propose a root-zone soil moisture estimation method utilizing a context-aware data clustering process, which can be applied prior to any statistical analysis, for empirical evaluation of data. In this aspect, the crops' phenological stages and soil-air temperature differences are defined as the two contexts for data clustering. Parameters such as canopy-air temperature difference, land surface temperature, and solar radiation with respect to plant energy and water processes are used for the analysis. The proposed model is utilized using piecewise linear regression of data obtained from 16 rainfed wheat parcels distributed across Turkey, under different climatic and topographic conditions. It is shown that the proposed context-aware data clustering process enables the nonlinear plant behavior to be analyzed linearly. The correlation value of the whole season increased from 21% to a range between 78% and 95% for different clusters. The outliers became relevant and the parameters became significant after the proposed context-aware data clustering.