Drinking water utilities may be required to change disinfectant to improve water quality and meet more stringent disinfection regulations. This research was conducted to assess and compares chlorine dioxide to free chlorine and chloramines on bacterial water quality monitored within model distribution systems (i.e., annular reactors). Following colonization with nondisinfected water, annular reactors containing either polycarbonate or cast iron coupons were treated with free chlorine, chlorine dioxide or chloramines. Two disinfectant doses (low/high) were tested for each disinfectant. Under specific environmental conditions, bacterial inactivation varied as a function of the disinfectant type and dose, sample type (bulk water versus biofilm bacteria) and coupon material. The ranking by efficiency was as follows: chlorine dioxide > chlorine > chloramines. On preformed biofilms of 106-107cfu/cm2, the continuous application of a disinfectant led to a log removal of heterotrophic bacteria concentrations for suspended and biofilm bacteria ranging from 1.1 to 4.0, and from 0.2 to 2.5, respectively. Doubling the amount of disinfectant doses led to an additional log inactivation of 1–2.5 of heterotrophic bacteria levels. This study demonstrates that bacterial inactivation in distribution systems is governed by various inter-related parameters. The data indicate that chlorine dioxide represents a viable alternative for secondary disinfection in distribution systems.