The spatiotemporal distribution characteristics of water and nitrogen in the soil profile are essential influencing factors that determine the development of crop root systems. The purpose of this study was to clarify the inter-row and inter-tree variability in soil moisture in the apple root zone, and to determine the effective root diameter ranges of apple trees that influence water and nitrogen absorption. The method used was a 2-year border irrigation experiment carried out in a traditional apple orchard in Zuncun, Shanxi Province, China. Dynamic variations in the soil moisture between trees within the row (perpendicular to the direction of border irrigation) and between rows (along the direction of border irrigation) were continuously measured from 2015 to 2016, and a specific soil profile was excavated to analyze the distribution characteristics of soil water, nitrogen, and roots with different diameters. The results showed obvious variations in soil moisture in the surface soil of 0–30 cm, and the soil moisture content between rows was 5% higher than that between trees within the row. The root length density in the soil between trees within the row was 33.5% higher than that in the soil between rows. Bivariate correlation analysis showed that the correlation between the root system and nitrogen and water was ranked from highest to lowest: total nitrogen (0.741) > nitrate nitrogen (−0.36) > soil moisture (−0.273). The correlation coefficient between trees within the row was higher than that between rows. Lower soil moisture between trees within the row resulted in increased root biomass and more active uptake activity between trees within the row. There were different significant correlations between the specific root diameter and the contents of soil water and nitrogen, showing that the 1.5 mm diameter roots correlated with the water content, whereas the 2.0 mm diameter roots correlated with the nitrogen content. The findings of this study provide a deeper understanding of the absorption mechanism of crop roots for soil water and nitrogen.