This study addresses the issue of the variability and heterogeneity problems that are expected from a sensor with a larger footprint having homogenous and heterogeneous sub-pixels. Improved understanding of spatial variability of soil surface characteristics such as land cover and vegetation in larger footprint are critical in remote sensing based soil moisture retrieval. This study analyzes the sub-pixel variability (standard deviation of subgrid pixels) of Normalized Difference Vegetation Index and SAR backscatter. Backpropagation neural network was used for soil moisture retrieval from active microwave remote sensing data from Southern Great Plains of Oklahoma. The effect of land cover heterogeneity (number of different vegetation species within pixels) on soil moisture retrieval using active microwave remote sensing data was investigated. The presence of heterogeneous vegetation cover reduced the accuracy of the derived soil moisture using microwave remote sensing data. The results from this study can be used to characterize the uncertainty in soil moisture retrieval in the context of Soil Moisture Active and Passive (SMAP) mission which will have larger footprint.