In high-resolution imagery, shadows may cause problems in object segmentation and recognition due to their low reflectance. For instance, the spectral reflectance of shadows and water are similar, particularly in the visible band. In precision agriculture, the vegetation condition in terms of plant water use, plant water stress, and chlorophyll content can be estimated using vegetation indices. Normalized Difference Vegetation Index (NDVI), Leaf Area Index (LAI) and Enhanced Vegetation Index (EVI) are widely used vegetation indices for characterizing the condition of the vegetation. In addition, many soil indices have been developed for describing soil characteristics, such as Soil-Adjusted Vegetation Index (SAVI). However, shadows can have an influence on the performance of these vegetation and soil indices. Moreover, enhancing spatial resolution heightens the impact of shadows in the imagery. In this study, the behavior of vegetation and soil indices are evaluated using four sets of high-resolution imagery captured by the Utah State University AggieAir unmanned aerial vehicle (UAV) system. These indices were obtained from flights conducted in 2014, 2015, and 2016 over a commercial vineyard located in California for the USDA Agricultural Research Service Grape Remote sensing Atmospheric Profile and Evapotranspiration Experiment (GRAPEX) Program. Different shadow restoration methods are used to alleviate the impact of shadows in information products that might be developed from the high-resolution imagery. The histogram pattern of vegetation and soil indices before and after shadow compensation, are compared using analysis of variance (ANOVA). The results of this study indicate how shadows can affect the vegetation/soil indices and whether shadow compensation methods are able to remove the statistical difference between sunlit and shadowed vegetation/soil indices.