Polyhexamethylene guanidine hydrochloride (PHMG) is an antibacterial polymer compound of increasing interest in water treatment, thanks to its strong activity and low toxicity. In this study, PHMG was synthesized by hot-melt polycondensation and used to prepare antibacterial composite beads with sodium alginate. The IR analysis results indicated that alginate/PHMG composite beads were successfully synthesized, and there is a chemical interaction between alginate and PHMG. Therefore, the composite has high stability, only 6.2% (wt.) of PHMG was released from the composite when it was soaked in water. The synthesized PHMG has excellent antibacterial activity against gram-positive (+) and gram-negative (-) bacteria and fungi, with a MIC value not exceeding 32 µg/mL. The water disinfection test showed that alginate/PHMG composite beads can material 100% of ~ 103 CFU/mL E.coli have been killed, and that composite can be reused 3 times.