An optimized disinfection method with metal ions to address cyanobacteria contamination in freshwater is presented, based on recyclable magnetic nanoparticles. In this study, the disinfection ability of individual metal ions (Ag+ and Cu2+) and combined (Ag+ + Cu2+) were evaluated with a target cyanobacteria, Oscillatoria tenuis, under various environmental conditions. The usage of combined Ag+ and Cu2+ reduces the time and concentration needed to achieve the same disinfection effectiveness compared to individual metal ions. However, the addition of Cu2+ and Ag+ stimulated production of cyanotoxin during disinfection, with an increase of 24.8% for anatoxin-a. To reduce the potential health risk, we evaluated the recovery and reuse of metal ions, and removal of cyanotoxins after disinfection, using magnetic nanoparticles with permanently confined micelle arrays (Mag-PCMA) under various environmental conditions. Recovery efficiency of Ag+, the most valuable ion, was excellent (99.8%), although it decreased to 74.5% with increasing Cl- concentration (0–10 mg/L). The regeneration and reuse of Mag-PCMA was studied for 5 cycles. Removal efficiency of Cu2+, anatoxin-a and cylindrospermopsin were minimally changed during the 5 sorption-desorption cycles, and that of Ag+ remained above 93% by the end of 5th cycle, indicating that this disinfection method may be sustainable for practical use with low energy requirements and minimized environmental impacts.