Accurate estimation of sub-surface properties such as moisture content and depth of soil and vegetation layers is crucial for applications spanning sub-surface condition monitoring, precision agriculture, and effective wildfire risk assessment. Soil in nature is often covered by overlaying vegetation and surface organic material, making its characterization challenging. In addition, the estimation of the properties of the overlaying layer is crucial for applications like wildfire risk assessment. This study thus proposes a Bayesian model-updating-based approach for ground penetrating radar (GPR) waveform inversion to predict moisture contents and depths of soil and overlaying material layer. Due to its high correlation with moisture contents, the dielectric permittivity of both layers were predicted with the proposed method, along with other parameters, including depth and electrical conductivity of layers. The proposed Bayesian model updating approach yields probabilistic estimates of these parameters that can provide information about the confidence and uncertainty related to the estimates. The methodology was evaluated for a diverse range of experimental data collected through laboratory and field investigations. Laboratory investigations included variations in soil moisture values, depth of the overlaying surface layer, and coarseness of its material. The field investigation included measurement of field soil moisture for sixteen days. The results demonstrated predictions consistent with time-domain reflectometry (TDR) measurements and conventional gravimetric tests. The depth of the surface layer could also be predicted with reasonable accuracy. The proposed method provides a promising approach for uncertainty-aware sub-surface parameter estimation that can enable decision-making for risk assessment across a wide range of applications.