Chloraminated drinking water systems commonly use free chlorine conversions (FCCs) to prevent or control nitrification, but unintended water quality changes may occur, including increased disinfection by‐product and metal concentrations. This study evaluated water quality in a chloraminated drinking water system and residential locations before, during, and after their annual, planned FCC. Water quality alternated between relatively consistent and variable periods when switching disinfectants. During the FCC, regulated four trihalomethane and five haloacetic acid concentrations increased by four and seven times, respectively, and exceeded corresponding maximum contaminant levels. Implications of disinfection by‐product sampling during an FCC were assessed, and an approach to account for increased FCC disinfection by‐product concentrations was proposed. For metals, the FCC had minor impacts on distribution system concentrations and did not appear to impact residential concentrations. Overall, observed variable water quality appeared primarily associated with switching disinfectants and depended on distribution system hydraulics.