Ecological restoration technologies have become effective measures for improving urban water systems. In this study, water quality monitoring, acute biological toxicity tests, and microorganism and antibioticresistance gene analyses were conducted to comprehensively understand the contribution of ecological restoration projects to improving the water quality of reclaimed water-replenishing urban rivers. The results showed that the concentrations of chemical oxygen demand (COD), total nitrogen, total phosphorus, and ammonia nitrogen (NH₄⁺-N) exhibited a downward trend along the flow direction throughout the ecological restoration engineering area. The amounts of NH₄⁺-N and COD were further reduced through ecological restoration engineering to approximately 75% and 35%, respectively. It demonstrates a notable mitigating effect on the acute biological toxicity of organisms, leading to a substantial rise in the half-inhibitory concentration for Luminous bacteria, Chlorella, and Daphnia magnas. The increases are observed within the ranges of 4.94 to 6.91 N, 10.85 to 46.04 N, and 2.98 to 5.80 N, respectively. In addition, it has a better control effect on pathogenic bacteria, drug-resistant bacteria, and antibiotic-resistance genes. Therefore, ecological restoration projects are more promising measures to further improve reclaimed water before the replenishment of urban rivers. This is an effective and feasible method to ensure the safety and quality of reclaimed water.