In freshwater samples, benzalkonium chloride (BAC) effectively prevents radiocarbon (14C) of dissolved inorganic carbon (DIC) from changing owing to its bactericidal effects. The addition of BAC is a promising alternative method to mercury, which is currently the standard method of sterilization. Therefore, it is important to investigate its basic potential in advance for radiocarbon observations in seawater if mercury is prohibited. Since the BAC efficiency decreases in seawater, our investigation focused on salinity, which is the distinguishing characteristic of seawater. The disinfectant effects of BAC in the low- and high-salinity (4.4 and 26.5) seawater samples at a constant BAC concentration and the varying BAC concentrations at a constant salinity (20.8) were examined. With BAC treatment, the higher-salinity samples exhibited larger changes in DIC 14C concentration and δ13C value, indicators of microbial activity, than the lower-salinity samples. At higher BAC concentrations (0.1% or 1%), DIC isotope values changed negligibly over time, whereas at the lower concentration (0.01%) they changed significantly over time. These findings suggest that salt diminishes the efficiency of BAC, potentially by degrading it, thereby reducing its bactericidal activity and allowing microorganism populations to recover, thus altering 14C concentration. Further, they indicate that increasing the BAC dosage may overcome its diminished efficacy in seawater samples.