Natural organic matter (NOM) is present in all raw water supplies and is the major precursor to chlorinated disinfection by‐products (DBPs). Reducing the amount of NOM entering treatment plants and better understanding the character of NOM in raw water supplies are essential for optimizing treatment and meeting more‐stringent regulations. A study of the unfiltered New York City (NYC) water supply system evaluated the extent to which alternative raw water selection strategies could reduce finished water DBP concentrations. A two‐year monitoring program was conducted to establish spatial and temporal patterns of DBP precursors in NYC's upstate reservoirs. System operations modeling was driven with a statistically generated, long‐term time series of dissolved organic carbon concentrations for each reservoir as a proof‐of‐concept evaluation of alternative operating rules to minimize precursor transport to terminal reservoirs. Results found that DBP precursors varied widely among reservoirs and over time but that modified reservoir operations could substantially reduce finished water DBP concentrations.