Disinfection residuals in drinking water protect water quality and public heath by limiting planktonic microbial regrowth during distribution. However, we do not consider the consequences and selective pressures of such residuals on the ubiquitous biofilms that persist on the vast internal surface area of drinking water distribution systems. Using a full scale experimental facility, integrated analyses were applied to determine the physical, chemical and biological impacts of different free chlorine regimes on biofilm characteristics (composition, structure and microbiome) and water quality. Unexpectedly, higher free chlorine concentrations resulted in greater water quality degredation, observable as elevated inorganic loading and greater discolouration (a major cause of water quality complaints and a mask for other failures). High-chlorine concentrations also reduced biofilm cell concentrations but selected for a distinct biofilm bacterial community and inorganic composition, presenting unique risks. The results challenge the assumption that a measurable free chlorine residual necessarily assures drinking water safety.