A method for stabilizing and removing Cryptosporidium oocysts or Giardia cysts from water. The method comprises adding chitosan, a salt or solution of chitosan to water containing Cryptosporidium oocysts or Giardia cysts and a halogenating agent. The method may also include adding a secondary polyelectrolyte flocculant to the water. The resulting flocs are filtered to remove the Cryptosporidium oocysts or Giardia cysts.