We examined the spatial structure of fruit yield, tree size, vigor, and soil properties for an established pear orchard using Moran’s I, geographically weighted regression (GWR) and variogram analysis to determine potential scales of the factors affecting spatial variation. The spatial structure differed somewhat between the tree-based measurements (yield, size and vigor) and the soil properties. Yield, trunk cross-sectional area (TCSA) and normalized difference vegetation index (NDVI, used as a surrogate for vigor) were strongly spatially clustered as indicated by the global Moran’s I for these measurements. The autocorrelation between trees (determined by applying a localized Moran’s I) was greater in some areas than others, suggesting possible management by zones. The variogram ranges for TCSA and yield were 30–45 m, respectively, but large nugget variances indicated considerable variability from tree to tree. The variogram ranges of NDVI varied from about 14–27 m. The soil properties copper, iron, organic matter and total exchange capacity (TEC) were spatially structured, with longer variogram ranges than those of the tree characteristics: 31–95 m. Boron, pH and zinc were not spatially correlated. The GWR analyses supported the results from the other analyses indicating that assumptions of strict stationarity might be violated, so regression models fitted to the entire dataset might not be fitted optimally to spatial clusters of the data.