From Emerging Infectious Diseases (http://www.cdc.gov/ncidod/EID/)
With waterfowl being significant carriers of H5N1, there are definite concerns about H5N1 being transmitted to other poultry and humans through water.
A recent study published in EID demonstrated that Chlorination, the most common form of water treatment, does indeed kill H5N1
"The results of this study confirm that avian influenza (H5N1) is readily inactivated by
chlorination... For drinking water disinfection at conditions similar to those used in this study, the US Environmental Protection Agency specifies free chlorine Ct values of 6 and 8 mg-min/L to achieve enteric virus inactivation of 3 and 4 orders of magnitude, respectively (14). According to our results, these Ct values would be more than sufficient to inactivate HPAI (H5N1) in the
water environment. The information on chlorine disinfection presented here should be helpful for developing risk management procedures regarding the role of water in the transmission of the virus to humans and poultry."
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