Elevated nitrate levels in natural water bodies significantly disrupt the global nitrogen cycle and pose a substantial environmental and human health risk. This study investigates the selective conversion of nitrate to ammonia via catalytic hydrogenation. This highly efficient and selective process offers a sustainable alternative to traditional ammonia production methods while simultaneously addressing nitrate pollution. Ruthenium (Ru) catalysts supported on ceria (CeO2), titania (TiO2), and tin dioxide (SnO2) were synthesized using a simple impregnation method, incorporating oxygen vacancies and low Palladium (Pd) loadings (0.25–0.5 wt%) to enhance catalytic performance. Ru-Pd/CeO2 exhibited superior activity and selectivity, maintaining near 100 % ammonia selectivity across various nitrate concentrations. At 75 °C, complete conversion of 2000 ppm nitrate to ammonia was achieved within 80 min using Ru-Pd/CeO2, and the yield of ammonia can reach up to 16440 mg•h−1•gRu-1. Subsequent ammonia enrichment through evaporation yielded pure ammonia solutions up to 3.6 wt%. Characterization and theoretical calculations suggest that abundant oxygen vacancies on the CeO2 surface and efficient hydrogen spillover from Pd nanoparticles synergistically contribute to the Ru-Pd/CeO2 catalyst’s superior performance. The catalyst exhibited excellent stability and reusability, maintaining high activity and selectivity over four cycles. This research presents a promising strategy for addressing nitrate pollution in water bodies while offering a sustainable and environmentally friendly route for ammonia synthesis. The findings of this study lay the foundation for further advancing and potentially implementing catalytic hydrogenation technology for nitrate pollution remediation and ammonia synthesis.