Introduction: Agricultural water scarcity and cadmium (Cd) contamination threaten global food security. Reclaimed water (RW) and partial root-zone alternate irrigation (PRA) offer possible solutions, but their synergistic effects on Cd-contaminated soils remain unclear. Objective: This study evaluated the impacts of PRA with RW on Cd-polluted tomato-growing soils. Methods: A pot experiment was conducted with 5 Cd levels (0.30–2.74 mg/kg, 5 replicates each). Soil properties, enzyme activities, Cd fractions, and 16S rRNA microbiome were analyzed. Results: PRA with RW increased rhizosphere pH by 0.42 units (p < 0.01), decreased EC by 18.7% (p < 0.05), and available Cd by 12.3% (p < 0.05). Catalase activity rose by 27.47% (p < 0.05), while sucrase and urease decreased by 32.1% and 28.5% (p < 0.01). Beneficial Actinobacteria (+8.26%) and Proteobacteria (+4.64%) were enriched, and Bacillus was reduced by 11.8%. Flavisolibacter (r = 0.802, p < 0.001) and Nocardioides (r = 0.572, p < 0.001) were key genera. Conclusions: PRA with RW reduces Cd bioavailability and ecological risks, providing a sustainable strategy for mildly/moderately polluted farmland soil.