Against the backdrop of intensifying global water scarcity, reclaimed water reuse has emerged as a critical strategy for ecological replenishment of landscape water bodies. However, its potential ecological risks remain underexplored. This study aims to establish a multidimensional ecological safety evaluation framework for reclaimed water replenishment systems and propose hierarchical risk prevention strategies. By integrating ecotoxicological assays (algae growth inhibition, Daphnia behavioral anomalies, zebrafish embryo toxicity), multimedia exposure modeling, and Monte Carlo probabilistic simulations, the risk contributions and spatial heterogeneity of typical pollutants are quantitatively analyzed. Results revealed that sulfamethoxazole (RQ = 2.3) and diclofenac (RQ = 1.8) posed high ecological risks, with their effects nonlinearly correlated with hydraulic retention time (HRT < 3 days) and nutrient loading (TN >1.2 mg/L). A three-tier risk prevention system was developed based on the “source-pathway-receptor” framework: ozone-activated carbon pretreatment achieved 85% removal efficiency for pharmaceutical contaminants, ecological floating beds enhanced nitrogen and phosphorus retention by 40%–60%, and hydraulic regulation (flow velocity > 0.1 m/s) effectively suppressed pathogen proliferation. The innovation of this study lies in establishing a chemical-biological-hydrological coupled risk quantification model for reclaimed water reuse scenarios. The hierarchical prevention standards have been incorporated into local reclaimed water management regulations, providing a scientific foundation and technical paradigm for sustainable landscape water replenishment.