Chlorine Dioxide has no known side effects, in fact, it is considered safer than most other disinfectants used in water.

Chlorine dioxide is a an excellent antimicrobial agent registered by the US  EPA for use in purifying drinking water and has been in use for many years.  It has been shown to kill microorganisms much more rapidly than chlorine and iodine while not producing harmful byproducts.  When used as directed at safe levels, chlorine dioxide breaks down quickly into water, oxygen and common table salt with no known harmful effects to humans or the environment.  Chlorine dioxide is a sanitizer of choice (approved by the FDA) in the food industry due to its effectiveness and safety and is the recommended water disinfection method by the US Centers for Disease Control for back country and travel use.