Control of protozoa and protozoan cysts that harbor legionella

Use of an effective amount of a phosphonium salt in the manufacture of a medicament for controlling protozoa trophozoite and cysts is disclosed, wherein the phosphonium salt is represented by formula (R1)3 P+ R2·X", wherein R1 is an alkyl group having from 1-8 carbons and R2 comprises an n-alkyl group having from 6-20 carbon atoms and X" is an anion selected form the group consisting of halides, sulfates, nitrates, nitrites and mixtures thereof. Addition of phosphonium salts such as Tri-n-butyl-tetradecylphosphonium chloride to aqueous systems was found to be effective at killing both the protozoa trophozoites and cysts. By effectively killing both the protozoa trophozoites and cysts, bacterial organism such as Legionella cells harboured in both the trophozoites and cysts are killed.