Root exploitation of soil heterogeneity and microbially mediated rhizosphere nutrient transformations play critical roles in plant resource uptake. However, how these processes change under water-saving irrigation technologies remains unclear, especially for organic systems where crops rely on soil ecological processes for plant nutrition and productivity. We conducted a field experiment and examined how water-saving subsurface drip irrigation (SDI) and concentrated organic fertilizer application altered root traits and rhizosphere processes compared to traditional furrow irrigation (FI) in an organic tomato system. We measured root distribution and morphology, the activities of C-, N-, and P-cycling enzymes in the rhizosphere, the abundance of rhizosphere microbial N-cycling genes, and root mycorrhizal colonization rate under two irrigation strategies. Tomato plants produced shorter and finer root systems with higher densities of roots around the drip line, lower activities of soil C-degrading enzymes, and shifts in the abundance of microbial N-cycling genes and mycorrhizal colonization rates in the rhizosphere of SDI plants compared to FI. SDI led to 66.4% higher irrigation water productivity than FI, but it also led to excessive vegetative growth and 28.3% lower tomato yield than FI. Our results suggest that roots and root-microbe interactions have a high potential for coordinated adaptation to water and nutrient spatial patterns to facilitate resource uptake under SDI. However, mismatches between plant needs and resource availability remain, highlighting the importance of assessing temporal dynamics of root-soil-microbe interactions to maximize their resource-mining potential for innovative irrigation systems.