Radiocarbon (14C) concentration and stable carbon isotopic ratio (σ13C) of dissolved inorganic carbon in natural waters are often utilized to elucidate carbon dynamics, hydrology, and biological activities. However, these values are susceptible to alterations caused by microbial activities, even within several days of sample preservation. To ensure accurate measurements by minimizing microbial interference, a disinfection process is required. Benzalkonium chloride (BAC) has emerged as a safer and more practical alternative to the conventional mercuric chloride for water preservation. Nonetheless, it has been observed that the BAC effect is reduced in seawater samples. This study aims to explore the influence of salt concentration in natural water as a potential suppressor of BAC effect, examining its impact on BAC effect using samples of two natural waters. Both high-salt and lowsalt concentration samples were prepared from seawater and groundwater, and the effectiveness of BAC in these sample was compared based on changes in 14C concentration and σ13C. The effectiveness of BAC in high-salt seawater samples was reduced by about one-seventh, to 30% in σ13C and 16% in 14C concentration, respectively, compared to low-salt seawater samples. On the other hands, the effectiveness of BAC did not shift significantly beyond the error range for the high-salt and low-salt groundwater samples. This suggests that salt concentration suppresses the BAC effect in seawater but has minimal influence on BAC effect in groundwater. This discrepancy could be attributed to differences in spore concentration in samples.