Abstract The measured concentrations of cadmium, cobalt, copper, nickel, lead, zinc, and manganese in acidified (pH<2) estuarine water samples analyzed for total dissolved trace metal concentrations using on-line chelating resin column partitioning with inductively coupled plasma-mass spectrometry (CRCP-ICP-MS) were compared to those analyzed by graphite furnace atomic absorption spectrometry (GFAAS) after liquid–liquid extraction using a combination of 1-pyrrolidinedithiocarbamate/diethyldithiocarbamate (PDC/DDC). Although there was good agreement between the two sets of analyses for cadmium, lead, manganese, and zinc concentrations, those of cobalt, copper, and nickel determined by CRCP-ICP-MS were found to be 10–20% lower than those determined by solvent-extraction GFAAS. The different yields were positively correlated ( R>0.961, simple linear regression) to the dissolved organic carbon (DOC) concentration of the samples. Good agreement between the two methods for cobalt and copper was achieved after ultraviolet (UV) digestion of the acidified samples. Samples collected from the South Bay of the San Francisco Estuary with high DOC showed the greatest difference for cobalt, copper, and nickel which is tentatively attributed to complexation with humic material for copper and cobalt and strong synthetic chelating agents such as ethylenediaminetetraacetic acid (EDTA) for nickel. This is consistent with previous studies on copper, nickel and cobalt complexation in this region. We recommend UV digestion of acidified estuarine samples prior to multi-element analysis by chelating resin flow injection ICP-MS methods.