Deep soil tillage and proper rootstock selection mitigate the root development limitations in Ultisol’s Bt horizon, enhancing the citrus yield potential. This study evaluates the root spatial distribution of three Ponkan tangerine rootstocks in Ultisol under deep tillage alongside the physical-hydric attributes and plant measurements. The experimental area underwent furrow creation, subsoiling, and hole opening for planting. The treatments included three rootstocks: “Cravo Santa Cruz” (CSC), “Sunki Tropical” (ST), and “Citrandarin Índio” (CI). Under the Ultisol preparation, these rootstocks were compared to a native forest area (FA). Three years post-initial tillage, soil samples were collected at depths of 0–0.05, 0.35–0.40, and 0.45–0.50 m from the pre-established positions. The evaluation encompassed soil dispersive clay, available water, crop water use, plant measurement, and crop yield. The root evaluation utilized the crop profile method and 2D images, with subsequent surface mapping of the root variables, number (NR), and diameter (RD) analyzed via kriging geostatistical analysis. The Ultisol showed significant changes in its physical-hydric attributes regarding structural change and more excellent clay dispersion, with a considerable contribution to the micropore volume. Deep tillage effectively improved the root spatial distribution, especially concerning the number and diameter of roots, and enhanced the water use, reflected in the vegetative growth and yield, with the rootstock CSC standing out.