Groundwater contamination by iron (Fe) and manganese (Mn) remains a persistent challenge in rural areas, where access to advanced treatment technologies is limited. Existing phytoremediation or natural coagulant methods are typically applied separately, resulting in slow removal rates and inconsistent efficiency. This study introduces a hybrid phyto-coagulation system that integrates Eichhornia crassipes with Moringa oleifera seed extract to accelerate metal removal through simultaneous biosorption, bio-oxidation, and protein-induced flocculation. A factorial Completely Randomized Block Design was used to evaluate combinations of plant biomass (0–30 leaves), moringa doses (0–100 mg/L), and treatment duration (0–16 days). Groundwater from nine wells in Margorejo Village, Indonesia, showed Fe and Mn levels exceeding WHO and national standards. Unlike conventional single-method approaches, the hybrid system demonstrated a synergistic removal pathway, achieving near-complete metal elimination. The optimal configuration (30 leaves + 100 mg/L, 16 days) reduced Fe to 0.082 mg/L (97.77%) and Mn to undetectable levels (98.71%). This study provides the first experimental evidence that coupling phytoremediation with natural coagulation significantly enhances metal removal kinetics, offering a scalable, low-cost treatment model for decentralized groundwater purification.