Seismic waves are filtered as they pass through soil layers, from bedrock to surface. Frequencies and amplitudes of the response wave are affected due to this filtration effect and this will result in different ground motion characteristics. Therefore, it is important to consider the impact of the soil properties on the evaluation of earthquake ground motions for the design of structures. Soil properties in a heterogeneous soil layer are affected by a series of uncertainties. Inherent variability of shear modulus contributing most to the overall uncertainty is described and modeled in this paper using deterministic and stochastic field representations. This paper highlights the importance of the effect of the stochastic components of the heterogeneity of shear modulus on response behavior of natural alluvial deposits in comparison to the deterministic consideration. The results emphasize that stochastic heterogeneity has significant effects in dynamic properties of natural alluvial deposits and its negligence would result in an over estimation of the fundamental frequency of spatially variable alluvial deposits.